Long term changes in aquatic plant communities in English lowland lakes

This thesis looks into the use of historical macrophyte records to assess long term changes in macrophyte communities in lakes and potential reasons for these changes. In particular it uses historical records to assess changes in macrophyte communities in the Norfolk Broads and West Midland Meres, two sets of lowland, eutrophic lakes in England. It provides a critical examination of the use of historical records, highlighting some of the constraints common to such data such as variations in recording effort, and bias in species recording and site selection. Having acknowledged these issues we then go on to develop a robust way to interpret such data, using a “change index” based on species persistence over the last 200 years within individual lakes. Species with high change index values, which represented species which had persisted or increased within the lake districts, were those known to be characteristic of eutrophic lakes. Conversely species with low index scores, which had declined in both the broads and meres over the last 200 years, included species associated with less fertile conditions but also a selection of typically eutrophic species. Averaging of change index scores in present day survey data served to identify the historically least changed lakes and to rank lakes in order of degree of botanical change over the last century. We then analysed the ecological basis of the change index in order to better understand the processes behind the decline of some species and survival of others in the Norfolk Broads and West Midland Meres. Functional groups determined from morphological and regenerative traits displayed significant differences in change index values in both groups of lakes, but declining taxa occurred across a wide range of plant growth forms. Non-hierarchical clustering of species based on their ecological preferences, obtained from published literature, resulted in groups with distinct change index values, indicating that changes in the status of species could be partly explained by these preferences. Of these, trophic preference was consistently the most important, with species of less fertile habitats consistently experiencing the greatest declines. However, some characteristically eutrophic species have also declined significantly, particularly in the broads. In these cases increasing loss of shallow water, low energy habitats in the broads, or loss of fluctuating water levels and less alkaline backwaters in the meres, appear to have been contributory factors. In addition to the change index approach, we also used historical records at a site level to complement palaeolimnological analysis and investigate the change in macrophyte community composition and structure at Barton Broad, Norfolk. Sediment samples were extracted from the bottom of the broad and analysed for sub-fossil remains and pollen of macrophytes. The historical records and palaeolimnological analysis combined showed that early communities did not consist entirely of low growing, oligotrophic and mesotrophic species as previously thought, but in fact comprised a mixture of these and other more characteristically high nutrient species associated with taller, or free-floating growth habit. As eutrophication progressed throughout the last century, the community was increasingly dominated by these latter growth forms. Diversity was maintained, however, since encroaching reedswamp generated a mosaic of low energy habitats which supported a range of species unable to withstand the hydraulic forces associated with more open water habitat. When the reedswamp disappeared in the 1950s, many of the dependent aquatic macrophytes also declined resulting in widespread macrophyte loss. The thesis demonstrates not just the complexities of using historical records, but also ways in which these can be overcome to make useful observations about macrophyte community change and lake ecological integrity to inform conservation and lake management, both on a site and lake district level.EThOS - Electronic Theses Online ServiceEnvironment AgencyStirling UniversityEnglish NatureBroads AuthorityGBUnited Kingdo

Will they be back? A framework to guide rare macrophyte conservation decisions in lakes

Shallow lake restoration typically focusses on the re-establishment of macrophytes. The likelihood of a species returning to a site is contingent on dispersal, proximity to propagule sources, and the on-site propagule-bank viability. We explore the potential of palaeoecological records in combination with botanical surveys and distribution maps, to ascertain the loss of three submerged macrophytes (Littorella uniflora, Najas flexilis, and Elatine hydropiper) from, respectively, two lakes (Barton Broad, Norfolk and Esthwaite Water, Cumbria) and one lake landscape (Greater Glasgow, Scotland). We discuss re-establishment likelihood when accounting for species' autoecology and current water-chemistry conditions. L. uniflora is widespread in the United Kingdom but absent locally in Norfolk without known seed bank, hence is unlikely to naturally recolonise Barton Broad. Furthermore, current conditions are unsuitable for this species suggesting that nutrient reduction is required prior to translocation. N. flexilis is extinct in Cumbria and the long distances involved (>100 km) for recolonisation of Esthwaite Water suggest that spatial dispersal is unlikely, rendering the seed bank the last chance of natural recovery. Alternatively, translocation may be feasible. E. hydropiper is a nationally scarce species in the United Kingdom yet would have only a short dispersal distance (~10 km) to recolonise Loch Libo, hence there being no requirement for translocation. In exploring the recovery possibilities for the three focal plant species, we develop a time–space integrated framework that can be employed to guide conservation decisions for other species, enabling a more rational use of translocations in the future, in line with international guidelines

100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report.

BACKGROUND: The U.K. 100,000 Genomes Project is in the process of investigating the role of genome sequencing in patients with undiagnosed rare diseases after usual care and the alignment of this research with health care implementation in the U.K. National Health Service. Other parts of this project focus on patients with cancer and infection. METHODS: We conducted a pilot study involving 4660 participants from 2183 families, among whom 161 disorders covering a broad spectrum of rare diseases were present. We collected data on clinical features with the use of Human Phenotype Ontology terms, undertook genome sequencing, applied automated variant prioritization on the basis of applied virtual gene panels and phenotypes, and identified novel pathogenic variants through research analysis. RESULTS: Diagnostic yields varied among family structures and were highest in family trios (both parents and a proband) and families with larger pedigrees. Diagnostic yields were much higher for disorders likely to have a monogenic cause (35%) than for disorders likely to have a complex cause (11%). Diagnostic yields for intellectual disability, hearing disorders, and vision disorders ranged from 40 to 55%. We made genetic diagnoses in 25% of the probands. A total of 14% of the diagnoses were made by means of the combination of research and automated approaches, which was critical for cases in which we found etiologic noncoding, structural, and mitochondrial genome variants and coding variants poorly covered by exome sequencing. Cohortwide burden testing across 57,000 genomes enabled the discovery of three new disease genes and 19 new associations. Of the genetic diagnoses that we made, 25% had immediate ramifications for clinical decision making for the patients or their relatives. CONCLUSIONS: Our pilot study of genome sequencing in a national health care system showed an increase in diagnostic yield across a range of rare diseases. (Funded by the National Institute for Health Research and others.)

Whole-genome sequencing of patients with rare diseases in a national health system

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 extensively phenotyped participants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data of UK Biobank participants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare