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  • 1
    ISSN: 1573-5133
    Keywords: mitochondrial DNA ; promoter sequence ; repeat units ; mtDNA evolution ; Rio Yaqui trout
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nucleotide sequences from the right-domain of salmonid mitochondrial DNA (mtDNA) control region flanking the phenylalanine tRNA gene (tRNAPhe) were determined for 5 species and 14 subspecies of Oncorhynchus at the southern extent of their range. In all but one population, the right domain contained two 72 bp tandem repeats located between the tRNAPhe gene and the conserved sequence block CSB-3. At the species level we found 46–83% homology between these two repeats. The repeat closest to tRNAPhe contained 43% of the phylogenetically informative sites. The largest number of transversions (N=6) were found outside of both repeat sequences. Phylogenetic inference based on mtDNA right-domain sequence was congruent with other analyses at the species level, but gave variable results in association drawn at the subspecific level. The right-domain contained three highly conserved sequences corresponding to the mtDNA transcription factor, and the heavy- and light-strand promoters. In four O. mykiss from Rio Yaqui, Mexico, the repeat containing the heavy-strand promoter (HSP) was deleted. The mtDNA HSP is responsible for transcription of the 16S and 12S rRNAs, 12 of the 13 protein-coding genes, and most of the tRNA genes. Rio Yagui trout showed no heteroplasmy or tissue specificity for this deletion. This HSP deletion suggests the possibility of a primitive transcriptional promoter with bidirectional capacity in this species, similar to that reported in avian and amphibian mtDNA. These data expand our understanding of genetic diversity in Oncorhynchus at the southern extent of their range with a knowledge of the evolutionary mechanisms that may have led to that diversity.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-5133
    Keywords: mitochondrial DNA ; promoter sequence ; repeat units ; mtDNA evolution ; Rio Yaqui trout
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nucleotide sequences from the right-domain of salmonid mitochondrial DNA (mtDNA) control region flanking the phenylalanine tRNA gene (tRNAPhe) were determined for 5 species and 14 subspecies of Oncorhynchus at the southern extent of their range. In all but one population, the right domain contained two 72 bp tandem repeats located between the tRNAPhe gene and the conserved sequence block CSB-3. At the species level we found 46–83% homology between these two repeats. The repeat closest to tRNAPhe contained 43% of the phylogenetically informative sites. The largest number of transversions (N=6) were found outside of both repeat sequences. Phylogenetic inference based on mtDNA right-domain sequence was congruent with other analyses at the species level, but gave variable results in association drawn at the subspecific level. The right-domain contained three highly conserved sequences corresponding to the mtDNA transcription factor, and the heavy- and light-strand promoters. In four O. mykiss from Rio Yaqui, Mexico, the repeat containing the heavy-strand promoter (HSP) was deleted. The mtDNA HSP is responsible for transcription of the 16S and 12S rRNAs, 12 of the 13 protein-coding genes, and most of the tRNA genes. Rio Yagui trout showed no heteroplasmy or tissue specificity for this deletion. This HSP deletion suggests the possibility of a primitive transcriptional promoter with bidirectional capacity in this species, similar to that reported in avian and amphibian mtDNA. These data expand our understanding of genetic diversity in Oncorhynchus at the southern extent of their range with a knowledge of the evolutionary mechanisms that may have led to that diversity.
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  • 3
    Publication Date: 2015-06-08
    Description: Coastal ecosystems provide numerous important ecological services, including maintenance of biodiversity and nursery grounds for many fish species of ecological and economic importance. However, human population growth has led to increased pollution, ocean warming, hypoxia, and habitat alteration that threaten ecosystem services. In this study, we used long-term datasets of fish abundance, water quality, and climatic factors to assess the threat of hypoxia and the regulating effects of climate on fish diversity and nursery conditions in Elkhorn Slough, a highly eutrophic estuary in central California (United States), which also serves as a biodiversity hot spot and critical nursery grounds for offshore fisheries in a broader region. We found that hypoxic conditions had strong negative effects on extent of suitable fish habitat, fish species richness, and abundance of the two most common flatfish species, English sole (Parophrys vetulus) and speckled sanddab (Citharichthys stigmaeus). The estuary serves as an important nursery ground for English sole, making this species vulnerable to anthropogenic threats. We determined that estuarine hypoxia was associated with significant declines in English sole nursery habitat, with cascading effects on recruitment to the offshore adult population and fishery, indicating that human land use activities can indirectly affect offshore fisheries. Estuarine hypoxic conditions varied spatially and temporally and were alleviated by strengthening of El Niño conditions through indirect pathways, a consistent result in most estuaries across the northeast Pacific. These results demonstrate that changes to coastal land use and climate can fundamentally alter the diversity and functioning of coastal nurseries and their adjacent ocean ecosystems.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 4
    Publication Date: 2015-08-01
    Print ISSN: 0308-597X
    Electronic ISSN: 1872-9460
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Political Science , Law
    Published by Elsevier
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  • 5
    Publication Date: 2021-04-01
    Description: Monitoring of environmental restoration is essential to communicate progress and improve outcomes of current and future projects, but is typically done in a very limited capacity due to budget and personnel constraints. Unoccupied aerial vehicles (UAVs) have been used in a variety of natural and human-influenced environments and have been found to be time- and cost-efficient, but have not yet been widely applied to restoration contexts. In this study, we evaluated the utility of UAVs as an innovative tool for monitoring tidal marsh restoration. We first optimized methods for creating high-resolution orthomosaics and Structure from Motion digital elevation models from UAV imagery by conducting experiments to determine an optimal density of ground control points (GCPs) and flight altitude for UAV monitoring of topography and new vegetation. We used elevation models and raw and classified orthomosaics before, during, and after construction of the restoration site to communicate with various audiences and inform adaptive management. We found that we could achieve 1.1 cm vertical accuracy in our elevation models using 2.1 GCPs per hectare at a flight altitude of 50 m. A lower flight altitude of 30 m was more ideal for capturing patchy early plant cover while still being efficient enough to cover the entire 25-hectare site. UAV products were valuable for several monitoring applications, including calculating the volume of soil moved during construction, tracking whether elevation targets were achieved, quantifying and examining the patterns of vegetation development, and monitoring topographic change including subsidence, erosion, and creek development. We found UAV monitoring advantageous for the ability to survey areas difficult to access on foot, capture spatial variation, tailor timing of data collection to research needs, and collect a large amount of accurate data rapidly at relatively low cost, though with some compromise in detail compared with field monitoring. In summary, we found that UAV data informed the planning, implementation and monitoring phases of a major landscape restoration project and could be valuable for restoration in many habitats.
    Electronic ISSN: 2296-665X
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Frontiers Media
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