Generalised procrustes analysis with optimal scaling: exploring data from a power supplier

Generalised Procrustes Analysis (GPA) is a method for matching several, possibly large, data sets by fitting them to each other using transformations, typically rotations. The linear version of GPA has been applied in a wide range of contexts. A non-linear extension of GPA is developed which uses Optimal Scaling (OS). The approach is suited to match data sets that contain nominal variables. A database of a Dutch power supplier that contains many categorical variables unfit for the usual linear GPA methodology is used to illustrate the approach

Robustifying multiple-set linear canonical analysis with S-estimator

In this paper, we consider a robust version of multiple-set linear canonical analysis obtained by using a S-estimator of covariance operator. The related influence functions are derived. Asymptotic properties of this robust method are obtained and a robust test for mutual non-correlation is introduced

Dedicated biomass crops can enhance biodiversity in the arable landscape

Suggestions that novel, non-food, dedicated biomass crops used to produce bioenergy may provide opportunities to diversify and reinstate biodiversity in intensively managed farmland have not yet been fully tested at the landscape scale. Using two of the largest, currently available landscape-scale biodiversity data sets from arable and biomass bioenergy crops, we take a taxonomic and functional trait approach to quantify and contrast the consequences for biodiversity indicators of adopting dedicated biomass crops on land previously cultivated under annual, rotational arable cropping. The abundance and community compositions of biodiversity indicators in fields of break and cereal crops changed when planted with the dedicated biomass crops, miscanthus and short rotation coppiced (SRC) willow. Weed biomass was consistently greater in the two dedicated biomass crops than in cereals, and invertebrate abundance was similarly consistently higher than in break crops. Using canonical variates analysis, we identified distinct plant and invertebrate taxa and trait-based communities in miscanthus and SRC willows, whereas break and cereal crops tended to form a single, composite community. Seedbanks were shown to reflect the longer term effects of crop management. Our study suggests that miscanthus and SRC willows, and the management associated with perennial cropping, would support significant amounts of biodiversity when compared with annual arable crops. We recommend the strategic planting of these perennial, dedicated biomass crops in arable farmland to increase landscape heterogeneity and enhance ecosystem function, and simultaneously work towards striking a balance between energy and food security

How has the morphology of the human mandible varied in response to the dietary changes that have occurred in Britain between the Neolithic and Post-Medieval periods?

Unlike cranial morphology, human mandibular morphology has been found to be influenced primarily by environmental as opposed to genetic factors. Previous research has demonstrated that significant morphological changes have occurred in the mandible during the Agricultural and Industrial Revolutions when widespread dietary changes occurred, and diet became softer. During this time the size of the mandible decreased, and mandible morphology became more gracile. This research however has typically focussed on comparisons between two time periods associated with a large dietary transition. For this reason, it is not known if the reported changes in mandible morphology represent a consistent reduction in mandibular robusticity or rather fluctuation between periods associated with dietary variability. Furthermore, it is unclear how susceptible the mandible is to smaller dietary changes. The aim of this thesis is to investigate how responsive mandible morphology is to the dietary changes that have occurred in Britain from the Neolithic through to the Post-Medieval periods. It is hypothesised that mandible morphology is responsive enough to mechanical stimuli that more minor dietary changes will also result in morphological variation. Results indicated that in general mandible morphology became increasingly gracile over time, while more pronounced morphological changes are associated with major dietary transitions such as the intensification of agriculture and the Industrial Revolution. Moreover, significant increases in gracilisation occurred between the Anglo-Saxon and Medieval period, potentially indicating that the dietary changes that occurred during the Industrial Revolution were more gradual than previous research has indicated. In addition to the more prominent morphological changes, smaller morphological fluctuations occurred such as during the Roman occupation. It is concluded that the mandible is more responsive to smaller dietary changes than demonstrated by previous research and the morphological variation associated with these major dietary transitions may not have been as simple or rapid as previously assumed

Determining normal and abnormal lip shapes during movement for use as a surgical outcome measure

Craniofacial assessment for diagnosis, treatment planning and outcome has traditionally relied on imaging techniques that provide a static image of the facial structure. Objective measures of facial movement are however becoming increasingly important for clinical interventions where surgical repositioning of facial structures can influence soft tissue mobility. These applications include the management of patients with cleft lip, facial nerve palsy and orthognathic surgery. Although technological advances in medical imaging have now enabled three-dimensional (3D) motion scanners to become commercially available their clinical application to date has been limited. Therefore, the aim of this study is to determine normal and abnormal lip shapes during movement for use as a clinical outcome measure using such a scanner. Lip movements were captured from an average population using a 3D motion scanner. Consideration was given to the type of facial movement captured (i.e. verbal or non-verbal) and also the method of feature extraction (i.e. manual or semi-automatic landmarking). Statistical models of appearance (Active Shape Models) were used to convert the video motion sequences into linear data and identify reproducible facial movements via pattern recognition. Average templates of lip movement were created based on the most reproducible lip movements using Geometric Morphometrics (GMM) incorporating Generalised Procrustes Analysis (GPA) and Principal Component Analysis (PCA). Finally lip movement data from a patient group undergoing orthognathic surgery was incorporated into the model and Discriminant Analysis (DA) employed in an attempt to statistically distinguish abnormal lip movement. The results showed that manual landmarking was the preferred method of feature extraction. Verbal facial gestures (i.e. words) were significantly more reproducible/repeatable over time when compared to non-verbal gestures (i.e. facial expressions). It was possible to create average templates of lip movement from the control group, which acted as an outcome measure, and from which abnormalities in movement could be discriminated pre-surgery. These abnormalities were found to normalise post-surgery. The concepts of this study form the basis of analysing facial movement in the clinical context. The methods are transferrable to other patient groups. Specifically, patients undergoing orthognathic surgery have differences in lip shape/movement when compared to an average population. Correcting the position of the basal bones in this group of patients appears to normalise lip mobility

Evolutionary relationships of East African soda lake cichlid fish

This thesis examines the evolutionary relationships of the Alcolapia soda lake cichlid fishes of East Africa. The introduction presents background on the soda lakes in which the cichlids are found, the taxonomy and biology of the fishes, as well as the theoretical background to the study. Chapter two discusses the methods used in the thesis, addressing the benefits and limitations of each, as well as their suitability to the study in hand. Chapter three investigates the phylogenetics and phylogeography of soda lake cichlids sampled at several populations around the soda lakes and a single transplanted population outside of the focal lakes, employing a large genomic dataset generated through restriction site associated DNA (RAD) sequencing, and demonstrates low levels of interspecific genomic differentiation with high levels of ongoing gene flow. Chapter four uses the RAD dataset to test for signals of selection between Alcolapia species, employing genome-wide scans and outlier detection to characterise peaks of genomic divergence between species. Chapter five combines morphological (geometric morphometrics) and ecological (stable isotope, stomach contents) data with the RAD dataset from chapter three to consider biologically relevant diversification between Alcolapia species, testing for convergence and niche adaptation. Chapter six examines the ecomorphology of the soda lake fishes at an intraspecific level, testing for effects of geography and environment on morphological differentiation between populations. Finally, chapter seven draws together the conclusions inferred from the thesis, and discusses possible future directions for research in this system

Geographic variation in the phenotype of an African horseshoe bat species, Rhinolophus damarensis, (Chiroptera: Rhinolophidae)

Studies involving geographic variation in the phenotypes of bats help scientists to explain why these mammals are the most species rich mammalian order second only to rodents, with well more than 1 300 species occurring worldwide. Such species richness or high diversity is the manifestation of the generation of biodiversity through the splitting of lineages within bat species. A lineage of bat species can diversify into several lineages which then differentiate from each other in allopatry. Thus, the spatial separation of a lineage into several lineages could be attributed to geographical, ecological and environmental factors across the distributional range of the species. Similarly, vicariant events may also play a role in separating lineages within species. The Damara horseshoe bat species, Rhinolophus damarensis, is widely distributed but restricted to the western half of southern Africa, where it occurs across several major biomes. Formerly regarded as the subspecies, R. darlingi damarensis, it was elevated to full species status on the basis of genetic and phenotypic differences between it and R. darlingi darlingi. Rhinolophus damarensis is itself made up of two ecologically separated genetic lineages. A total of 106 individuals of R. damarensis were sampled from seven localities across its distributional range, with a view to determining and documenting the extent of geographic variation in body size, echolocation parameters, wing parameters, cranial shape and postcranial morphology of individuals from populations of R. damarensis across the distributional range of the species. Firstly, an investigation into geographic variation in resting echolocation frequency (RF) of the horseshoe bat species, R. damarensis was carried out in the western half of southern Africa (Chapter 2). Three hypotheses were tested. The first one, James’Rule (JR), states that individuals occurring in hot humid environments generally have smaller body sizes than conspecifics that occur in cooler, dryer environments, and the largest are expected to occur in cool, dry areas. On this basis and because of the known relationship between body size and RF, it was predicted that there should be a correlation between body size and climatic factors and between body size and RF. The second hypothesis was Isolation by Environment (IbE) mediated through sensory drive, which proposes that diversification of lineage may be driven by environmentally-mediated differences in sensory systems. Under this hypothesis, it was predicted that call frequency variation should be correlated with climatic variables. The third hypothesis was that Isolation by Distance (IbD) can influence phenotypic trait variation by restricting gene flow between populations. Under the Isolation by Distance (IbD) Hypothesis, it was predicted that call frequency variation should be partitioned in accordance with geographic distance between populations. To investigate the probability of the JR, IbE and IbD, the Akaike’s information criterion AICc candidate models were evaluated with different combinations of environmental (annual mean temperature and relative humidity), spatial (latitude and region) and biological (forearm as a proxy for body size) predictor variables to determine their influence on resting frequency (RF) across the distributional range of R. damarensis. Linear mixed effects models (LMEs) were employed to analyse the relationship between the response variable (RF) and the environmental, spatial and biological predictor variables. The influence of prey detection range and atmospheric attenuation was also investigated. The results showed no evidence for JR or for random genetic drift. Body size was neither correlated with RF nor environmental variables, suggesting that variation in RF was not the result of concomitant variation in body size as proposed by JR. Similarly, the Mantel test showed no IbD effect and there was therefore no evidence that genetic drift was responsible for the variation in RFs. In contrast, the LMEs showed that there was support for IbE in the form of an association between RF and region (in the form of the variable “Reg”) which was based on the two geographically separated genetic lineages. Furthermore, RF variation was also associated with the climatic variable AMT. The taxonomic status of R. damarensis was investigated using ecological traits and phenotypic characters including skulls, wings and echolocation (Chapter 3) and three dimensional (3D) scanned skulls and mandibles (Chapter 4). The main objective (Chapter 3 and Chapter 4) was to test whether previously reported genetic divergence between the two R. damarensis lineages was associated with phenotypic divergence. Morphometric and echolocation measurements were taken from hand held individual bats in the field, and skull measurements were taken from field collected voucher specimens as well as museum specimens. Discriminant Function Analyses (DFA) revealed that there was geographic variation among populations and lineages of R. damarensis. Multivariate Linear Regressions (MLV) and Linear models (LM) on the basal parts of bacula revealed significant differences between the southern and northern lineages of R. damarenis. The bacula of the two lineages of R. damarensis appear to have different shapes. Diversification through shape analyses (Chapter 4) was investigated using three dimensional (3D) geometric morphometric analyses based on X-ray microcomputed tomography (µCT) scanning of dried skulls and mandibles of R. damarensis. Procrustes Anova results of both mandibles and skulls indicated that there were no significant differences between sexes but that the shape of skulls and mandibles varied across different localities (Chapter 4). Canonical Variate Analysis (CVA) suggested that geographic variation in R. damarensis mandibles was based on the shape and thickness of the alveolar bone. Geographic variation in the skulls was based on changes in the rostrum, anterior medial swelling and brain case. Some populations had slightly deeper rostra, slightly larger anterior medial swellings and smaller braincases, whilst others had slightly shallower rostra, slightly smaller anterior medial swellings and larger braincases. The northern lineage was found to be separated from the southern lineage based on the changes in skull and mandible shape. Therefore, separation of lineages within R. damarensis (Chapter 4) could be associated with the foraging and feeding behaviour of the species under different ecological conditions due to ecological opportunity. Overall, differences in the RF were found to be associated with Isolation by Environment mediated through sensory drive and this has led to the formation of two regional (northern and southern) groupings in RF (Chapter 2). The two lineages were supported by both the phenotypic divergence (Chapter 3) and shape variation within R. damarensis skulls and mandibles (Chapter 4). Thus, phenotypic differences corresponded to genetic differences between the two lineages and provide support for IbE

The consequences of phenotypic plasticity on postglacial fishes

Phenotypic differences within a species significantly contribute to the variation we see among plants and animals. Plasticity as a concept helps us to understand some of this variation. Phenotypic plasticity plays a significant role in multiple ecological and evolutionary processes. Because plasticity can be driven by the environment it is more likely to produce beneficial alternative phenotypes than rare and often deleterious genetic mutations. Furthermore, differences in phenotypes that arise in response to the environment can affect multiple individuals from the same population (or entire populations) simultaneously and are therefore of greater evolutionary significance. This allows similar, beneficial alternative phenotypes to increase quickly within a single generation and allow new environments to produce and select for new phenotypes instantly. The direction of the present thesis is to increase our understanding of how phenotypic plasticity, coupled with contrasting environmental conditions, can produce alternative phenotypes within a population. Plasticity provides a source of variation for natural selection to act upon, and may lead to genetic isolation as a by-product. For example, there are multiple cases of polymorphic populations of fish, where groups belonging to multiple isolated gene pools, have arisen in sympatry. Here it is shown that although plasticity is important in sympatric speciation events, plasticity alone is not responsible for the frequency in which sympatric polymorphic populations occur. The most frequently observed differences among sympatric polymorphic populations are morphological differences associated with parts of the anatomy used in the detection, handling and capture of prey. Moreover, it is shown here that there are physiological effects associated with foraging on alternative prey that may significantly contribute towards ecological speciation. It is also shown in this study that anthropogenic abiotic factors can disrupt developmental processes during early ontogeny, significantly influencing morphology, and therefore having ecological consequences. Phenotypic structuring in postglacial fish is most frequently based around a divergence towards either pelagic or littoral benthic foraging specialisms. Divergences that deviate from this pattern are of greater scientific interest as they increase our understanding of how evolutionary processes and selection pressures work. Here we describe a rare divergence not based around the typical pelagic/littoral benthic foraging specialisms. Finally, in this study, the effectiveness of local level conservation policy shows that species of fish which are highly variable in their life history strategies are harder to effectively manage and often poorly represented at a local level