1,243 research outputs found
Additional files for 'DNA sonification for public engagement in bioinformatics'
No full textSupplementary data for Plaisier H, Meagher TR and Barker D, 'DNA sonification for public engagement in bioinformatics' (under revision). For further details, see 'README.txt' within the zipfile.Plaisier, Heleen; Meagher, Thomas R; Barker, Daniel. (2021). Additional files for 'DNA sonification for public engagement in bioinformatics', [software]. University of Edinburgh. School of Biological Sciences. Institute of Evolutionary Biology. https://doi.org/10.7488/ds/3058
Additional files for 'Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments'
No full textSupplementary data for Martin EJ, Meagher TR and Barker D, 'Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments' (under revision). See 'README.pdf' for further details.Martin, Edward J; Meagher, Thomas R; Barker, Daniel. (2021). Additional files for 'Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments', [software]. University of Edinburgh. School of Biological Sciences. Institute of Evolutionary Biology. https://doi.org/10.7488/ds/3023
Range-wide analysis of the spatial distribution and genetic diversity of Delonix s.l. (Leguminosae) in Madagascar : enhancing herbarium-based conservation assessments
No full textDespite their ecological and economic importance, the majority of plant species and
their conservation status are poorly known. Only 4% of plants have been assessed
globally and listed on the IUCN Red List of Threatened Species; and without plant
conservation assessments, many plant species will not feature in conservation
planning.
Herbarium collection information can significantly increase the number of plant
conservation assessments. Thus, the aims of this thesis were: (1) to investigate how
the quality of herbarium-based conservation assessments can be optimised; (2) to
assess the extent to which herbarium-based conservation assessments reflect the
reality on the ground; and (3) to scientifically validate genetic and spatial underpinning
of IUCN criteria.
Preliminary range-based assessments of the Leguminosae of Madagascar achieved a
result consistent with the final conservation rating for over 95% of species when using
up to fifteen herbarium specimens. Bioclimatic modelling of range shifts based on
future climate change predicted that, in the worst case scenario, up to one third of
endemic Leguminosae in Madagascar will be threatened with extinction over the next
100 years. An analysis of the population structure of species of Delonix s.l.
(Leguminosae) showed that combining spatial analysis with population genetic data
provides a more complete picture of landscape-level population dynamics and the
impacts on conservation status.
Moreover, range-wide genetic analysis of AFLP markers for four species of Delonix
demonstrated a genetic basis for IUCN categories distinguishing between threatened
and non-threatened species. Although genetic data are currently not often
incorporated in conservation assessments, they are crucial in making accurate
management decisions and creating effective action plans for conservation. Only by
using all available scientific resources can informed conservation decisions be made
and the survival of plants and their associated ecosystems be ensured
Additional files for 'DNA sonification for public engagement in bioinformatics'
No full textSupplementary data for Plaisier H, Meagher TR and Barker D, 'DNA sonification for public engagement in bioinformatics' (2021, BMC Research Notes 14:243, doi:10.1186/s13104-021-05685-7). For further details, see 'README.txt' within the zipfile.See 'README.txt' file within the zipfile
SUPERSEDED - Additional files for 'DNA sonification for public engagement in bioinformatics'
No full text## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/3058 ##
Supplementary data for Plaisier H, Meagher TR and Barker D, 'DNA sonification for public engagement in bioinformatics' (in prep.). For further details, see 'README.txt' within the zipfile.See 'README.txt' file within the zipfile
Student Comments
No full textComments on court cases by Jon R. Robinson, Leslie L. Clune, Joanne M. Frasca, Timothy J. McDevitt, Thomas Stalzer, Susan Finneran, William J. Brooks, III, Richard James Annen, Patricia S. Higgins, Jane M. Grote, Martin J. Hagan, Roger P. Balog, Bruce Meagher, Joseph L. Baldino, John E. Glennon, John Gaal, Joseph V. Rizzi, and Michael T. Bierman
Additional files for 'Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments'
No full textSupplementary data for Martin EJ, Meagher TR and Barker D, 'Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments' (2021, BMC Bioinformatics 22:456, doi:10.1186/s12859-021-04362-7). See 'README.pdf' for further details.See 'README.pdf' file
A comparative investigation of nuclear DNA content and its phenotypic impacts in Silene marizii and S. latifolia
No full textConsiderable variation exists both within and between species in nuclear DNA content. Despite there being no obvious functional role for much of this DNA, many studies have reported phenotypic correlations with genome size at various taxonomic levels. This suggests that DNA plays a functional role beyond the traditionally understood mechanisms. One such example of a phenotypic correlation with DNA content is present in the genus Silene, where a negative correlation between DNA content and flower size exists within and between species. This relationship is consistent with the direction of sexual dimorphism in DNA content (caused by heteromorphic sex-chromosomes) and flower size in the most studied species in the genus: S. latifolia.
This thesis takes a comparative approach between two closely related species in the genus (S. latifolia and S. marizii), which differ markedly in their nuclear DNA content, in order to investigate the nature and phenotypic impacts of variation in DNA content.
A phenotypic survey from a number of S. marizii populations reveals that the pattern of DNA content variation in this species is very different to that in S. latifolia. In particular, phenotypic correlations with DNA content appear be much weaker, whilst sexual dimorphism in DNA content, when present, appears to occur in either direction. A survey of interspecific hybrids suggests that this may be due to an enlarged S. marizii X-chromosome and that DNA content in hybrids may be biased with regard to their parents. Repetitive elements may be significant constituents of plant genomes. A study of Ty1-copia class retrotransposons in the two species reveals that they are present as a large and highly heterogeneous population. Phylogenetic analysis of these elements suggests a substantial degree of genetic isolation between the two species. Finally, an assessment of the flow-cytometric method, used to estimate DNA content, reveals substantial error associated with the method, but only limited evidence for stoichiometric effects
Sex allocation and reproductive success in the andromonoecious perennial, Solanum carolinense (Solanaceae). II. paternity and functional gender
No full textThe work was supported by a National Science Foundation Doctoral Dissertation Improvement grant (DEB‐9411513), by the Society for Sigma Xi, and by a Hutcheson Memorial Forest grant.According to Bateman's principle, male fitness in entomophilous plant species should be limited by mating opportunity, which is influenced by the size or number of flowers. We determined male-specific fitness consequences of floral phenotype in andromonoecious Solanum carolinense, examined the relationship between male and female reproductive success within plants, and evaluated the distribution of functional gender among plants. A maximum likelihood-based paternity analysis, based on multilocus allozyme phenotypes of parents and offspring from four experimental plots, was used to determine male reproductive success and its relationship to floral phenotype. Male success was enhanced by an increase in the proportion of male flowers produced but not by an increase in total flower number, even though all flowers contain male parts. Larger flower size increased male success in only one plot. Male and female reproductive success were negatively correlated, and plants varied in functional gender from completely female to completely male. This gender specialization may occur because hermaphroditic and male flowers differ in their ability to contribute to male and female success. Although sex allocation theory predicts a positive relationship between the size or number of plant parts and reproductive success, this study indicates that aspects of floral morphology that affect gender specialization should also be considered.Peer reviewe
SUPERSEDED - Additional file for 'Efficient comparison of evolutionary trees during phylogenetic reconstruction'
No full text## This item has been replaced by the one which can be found at https://datashare.ed.ac.uk/handle/10283/4798 ##. Supplementary data for Guscott JC, Kim CS, Pinheiro M, Wood C, Winn MD, Guntoro F, Meagher TR, Barker D, 'Efficient comparison of evolutionary trees during phylogenetic reconstruction' (in prep.). For further details, see 'README.txt' within the zipfile.See 'README.txt' within the zipfile
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