Damming the genomic data flood using a comprehensive analysis and storage data structure

Data generation, driven by rapid advances in genomic technologies, is fast outpacing our analysis capabilities. Faced with this flood of data, more hardware and software resources are added to accommodate data sets whose structure has not specifically been designed for analysis. This leads to unnecessarily lengthy processing times and excessive data handling and storage costs. Current efforts to address this have centered on developing new indexing schemas and analysis algorithms, whereas the root of the problem lies in the format of the data itself. We have developed a new data structure for storing and analyzing genotype and phenotype data. By leveraging data normalization techniques, database management system capabilities and the use of a novel multi-table, multidimensional database structure we have eliminated the following: (i) unnecessarily large data set size due to high levels of redundancy, (ii) sequential access to these data sets and (iii) common bottlenecks in analysis times. The resulting novel data structure horizontally divides the data to circumvent traditional problems associated with the use of databases for very large genomic data sets. The resulting data set required 86% less disk space and performed analytical calculations 6248 times faster compared to a standard approach without any loss of information

The fluviageny, a method for analyzing temporal river fragmentation using phylogenetics

textPhylogenetic trees have historically been used to determine evolutionary relatedness between organisms. In the past few decades, as we've developed increasingly powerful computational algorithms and toolsets for performing analyses using phylogenetic methods, the use of these trees has expanded into other areas, including biodiversity informatics and geoinformatics. This report proposes using phylogenetic methods to create "fluviagenies" - trees that represent the effects of river fragmentation over time caused by damming. Faculty at the Center for Research in Water Resources at the University of Texas worked to develop tools and documentation for automating the creation of river segment codes (a.k.a., "fluvcodes") based on spatiotemporal data. Python was used to generate fluviageny trees from lists of these codes. The resulting trees can be exported into the appropriate data format for use with various phylogenetics programs. The Fishes of Texas Database (fshesoftexas.org), a comprehensive geospatial database of Texas fish occurrences aggregated and normalized from 42 museum collections around the world, was employed to create an example of how this tool might be used to analyze and hypothesize changes in fish populations as a consequence of river fragmentation. Additionally, this paper serves to theorize and analyze past and future potential uses for phylogenetic trees in various other fields of informatics.Informatio

Population genetics and genomics within the genus \u3ci\u3ePityopsis\u3c/i\u3e

Pityopsis (Asteraceae) includes seven species; one species, P. ruthii, is federally endangered. The genus exhibits a range of ploidy levels, widespread hybridization among species with overlapping ranges, and interesting adaptive traits such as fire-stimulated flowering. However, taxonomy of Pityopsis has remained unresolved. Resolving interspecific relationships can lead to a deeper understanding of the inheritance and hybridization patterns, as well as the evolution of adaptable traits. Our first objective was to examine population structure and gene flow within Pityopsis ruthii. Polymorphic microsatellite markers (7 chloroplast and 12 nuclear) were developed and used to examine genetic diversity of 814 P. ruthii individuals from 33 discrete locations along the Hiwassee and Ocoee Rivers. A total of 198 alleles were detected with the nuclear loci and 79 alleles with the chloroplast loci. Bayesian cluster analyses of both rivers identified six clusters when the chloroplast microsatellites were used, whereas only two clusters were identified from the nuclear microsatellites. The population structure of P. ruthii will allow delineation of conservation units that account for subpopulations along each river. Our second objective was to examine the relationships of the seven species within Pityopsis using phylogenetic analyses. The chloroplast genome was sequenced for six species and two varieties. A reference chloroplast genome was assembled de novo from P. falcata, the species with the highest depth of read coverage. Reads from seven other individuals were then aligned to the P. falcata chloroplast genome and an individual genome was assembled for each. To utilize all informative sites for the full length of the chloroplast, a multiple sequence alignment of the eight chloroplast genomes was constructed, and from this, a phylogeny using both the maximum likelihood and maximum parsimony methods. Our findings using the entire chloroplast genome deviate from the results of previous phylogenetic studies of Pityopsis and do not support previously defined clades or sections within the genus. Our two objectives add meaningful information about the diversity of P. ruthii and the evolutionary history of Pityopsis, now available for use by conservationists, molecular ecologists, and evolutionary biologists

Above- and below-ground biodiversity responses to the prolonged flood pulse in central-western Amazonia, Brazil

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Effects of Impoundments on the Community Assemblage and Gene Flow of Stream Crayfishes

Dams and their impoundments block movement of stream organism and change stream physiochemical properties, which subsequently changes biological assemblages and creates barriers to gene flow. While changes in species assemblages and gene flow have been assessed for numerous impoundments and stream organisms, no study has assessed the effects of large impoundments on crayfish assemblages and population genetic diversity and connectivity. I examined the physiochemical, biological, and genetic effects of impoundments on crayfishes. Between May 2015 and August 2017, I sampled multiple sites up- and downstream of three impounded streams, and along the lengths of two unimpounded streams, in the Bear Creek and Cahaba River drainages in Alabama, USA. First, I assessed the most effective sampling methods for collecting crayfishes in high gradient southern Appalachian streams. A combination of kick seining and electroshocking were most effective at collecting crayfishes, with higher species richness and decreased sampling biases when using both methods. Once effective methods were established, I assessed the effects of impoundments and their subsequent changes to crayfish assemblages and their habitats. Impoundments altered crayfish assemblages up- and downstream of impoundments. Crayfish abundances and species diversity were lower in impounded than unimpounded streams. Assemblages up- and downstream of impoundments were similar, but in unimpounded streams, gradual shifts in dominant species occurred from up- to downstream. Assemblage differences between impounded and unimpounded streams were associated with more stable temperature and flow regimes, decreases in crayfish refuge habitats (i.e., aquatic vegetation, interstitial space), and increased abundances of predatory fishes in impounded streams. Nonetheless, with distance downstream of impoundments, crayfish assemblages began to recover and resemble unimpounded stream assemblages. Impoundments also impacted gene flow and genetic structure of crayfishes. Impounded streams’ crayfish populations were genetically isolated, and unidirectional downstream gene flow, or no gene flow, was detected between up- and downstream populations. The degree of impact of impoundments on gene flow was species-specific, with intrinsic biological and life history characteristics, such as dispersal ability and physiological tolerance, determining the degree of impact. With already declining crayfish populations, decreases in species and genetic diversity due to impoundments can decrease the persistence of hundreds of crayfish species in thousands of impounded streams. These changes in crayfish populations can cause cascading effects throughout stream ecosystems by altering the numerous ecosystem services provided by crayfishes

Comparison of statistical algorithms for detecting homogeneous river reaches along a longitudinal continuum

International audienceSeven methods designed to delineate homogeneous river segments, belonging to four families, namely -- tests of homogeneity, contrast enhancing, spatially constrained classification, and hidden Markov models -- are compared, firstly on their principles, then on a case study, and on theoretical templates. These templates contain patterns found in the case study but not considered in the standard assumptions of statistical methods, such as gradients and curvilinear structures. The influence of data resolution, noise and weak satisfaction of the assumptions underlying the methods is investigated. The control of the number of reaches obtained in order to achieve meaningful comparisons is discussed. No method is found that outperforms all the others on all trials. However, the methods with sequential algorithms (keeping at order n + 1 all breakpoints found at order n) fail more often than those running complete optimisation at any order. The Hubert-Kehagias method and Hidden Markov Models are the most successful at identifying subpatterns encapsulated within the templates. Ergodic Hidden Markov Models are, moreover, liable to exhibit transition areas

Black spot disease in freshwater fishes of south-western Australia: identification of the parasite, host range and potential as a bioindicator for water quality

The salinisation of freshwater ecosystems by anthropogenic influences is recognised as one of the largest threats to the highly endemic freshwater fish fauna of south-western Australia. There has also been some recent evidence that secondary salinisation is affecting the parasite community of freshwater fishes. A parasitic trematode, which causes black spot disease in the musculature of native fishes, has previously been tentatively identified as Diplostomum galaxiae, a species first described from a galaxiid fish (Galaxias auratus) in Tasmania. The aims of the current study were to confirm this specific identification using genetic analyses; investigate the host and geographic range of the parasite in south-western Australia; and determine whether the parasite could be a suitable bioindicator of secondary salinisation. Encysted metacercariae were extracted from preserved fishes in the collection of the Freshwater Fish Group & Fish Health Unit, Murdoch University, and from a specimen of Galaxias truttaceus from Tasmania, and a section of the 18S rRNA gene sequenced. All parasites from south-western Australia and Tasmania were genetically identical, but did not group with other species in the Diplostomum genus in phylogenetic analyses. Instead, the Australian parasite aligned more closely to a clade containing Posthodiplostomum spp., and several genera from the Strigeidae family. Reclassification of the parasite causing black spot disease in south-western Australian freshwater fishes is thus recommended, following more extensive comparisons with the parasite throughout Australia. In the interim, the parasite has been designated with the temporary name Dip01. Historical collections of fishes from the West Australian Museum and from the Freshwater Fish Group & Fish Health Unit, Murdoch University were assessed, to collate records of Dip01 metacercariae. The parasite appears to preferentially infect Galaxias maculatus and Galaxias occidentalis over other species; although it was also found in two percichthyids (a single Nannatherina balstoni and several Bostockia porosa from a single catchment) and has been reported previously from two estuarine fishes (Leptatherina wallacei and Pseudogobius olorum) that have colonised secondarily salinised rivers of the region. The overall prevalence of Dip01 in G. maculatus was 11.7% (95% CI 9.3-14.4%), and in G. occidentalis was 6.1% (4.8-7.7%). The mean intensity of infection in G. maculatus was 3.5 (2.0-7.3) parasites/infected fish, while the mean intensity in G. occidentalis was 7.8 (5.9-10.3) parasites per infected fish. The geographic range of Dip01 closely matches that of the preferred hosts, G. maculatus and G. occidentalis. Prevalence and intensity data were compared against historical environmental data from the Water Information Reporting database of the Department of Water and Environmental Regulation, where available. There was a significant inverse relationship between parasite prevalence and salinity, with Dip01 only occurring in habitats with a conductivity of less than 1,000 μS/cm. Based on these data, the parasite appears to be a useful bioindicator of salinity, as it is restricted to low salinity waters, even though its preferred galaxiid hosts are tolerant of a wide range of salinities

Positive Interactions in Freshwater Systems

The goals of this thesis are twofold, 1) to review the existing literature on positive interactions, and 2) to experimentally test the role of biotic context in a freshwater reproductive interaction. First, my co-authors and I have conducted a review of positive interactions in freshwaters to establish a direction for future research. By outlining case studies and causal mechanisms, we illustrate the diversity of positive interactions, and set the stage for a comprehensive look at the role of context in shaping interaction outcomes. Our research directive focuses on the value of both basic life history and experimental research, then using those findings to investigate these interactions under different contexts, in different levels of ecosystem structure, and at multiple geographic scales. Applications of positive interactions are discussed in regards to conservation, restoration, biological invasions, and in aquaculture production. Following this review, I experimentally investigate context dependency in the nest associative interaction between two stream fishes. By using three treatments of partner density while maintaining otherwise consistent conditions, shifts in interaction outcomes can be directly attributed to context dependency. Findings are incorporated into our understanding of this novel study system, and their contribution to broader ecological theory is discussed

Characterizing freshwater macroinvertebrates of Bangladesh using metagenetic techniques

The degradation of freshwater ecosystems has become a global concern, in particular, the critical conditions of rivers in Bangladesh demand a monitoring programme through the assessment of bioindicator organisms. Macroinvertebrates as prominent bioindicators are widely used for assessing the health of aquatic ecosystems. Recent technological advances have enabled routine assessment with the genomic characterization of macroinvertebrates using different metagenetic techniques such as DNA barcoding for individual specimen identification, metabarcoding for multi-species identification of bulk samples and mitochondrial metagenomics for extraction of mitogenomes from mixed samples. In this thesis, I commence by generating Cytochrome Oxidase subunit (COI) barcodes for Bangladeshi freshwater macroinvertebrates belonging to the Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, Hemiptera, Odonata, Diptera, Gastropoda and Bivalvia. These barcodes can be used as a DNA reference library for species identification in metabarcoding of macroinvertebrates. I also aim for exploring complete mitogenomes from selected macroinvertebrates using a mitochondrial metagenomic pipeline. I carry out phylogenetic analysis with protein-coding genes that reveals the evolutionary relationship of Bangladeshi macroinvertebrate lineages and also support deeper level identification of barcodes placing them into the phylogenetic tree (chapter 2). In chapter 3, I assess some methodological aspects of the metabarcoding pipeline required for diversity estimation from complex bulk samples of macroinvertebrates in large-scale biomonitoring programmes. These include preparation of bulk macroinvertebrate samples, optimization of the procedure of homogenization of samples required for DNA extraction, strategies for DNA pooling from these extracts, choice of robust universal primers, and viable OTU clustering for reliable diversity estimation. The results have implications for the optimization and standardization of these steps in metabarcoding of freshwater macroinvertebrates. In chapter 4, I apply the metabarcoding technique to establish the macroinvertebrate diversity and impact of various types of anthropogenic disturbances on the freshwater macroinvertebrates in highland and lowland rivers. The results document high diversity, local endemicity and pronounced responses to disturbance in largely unexplored but threatened habitats of Bangladesh. My investigations manifest the viability of metagenetic techniques for applied conservation management as a step towards building a biomonitoring system in freshwater ecosystems globally.Open Acces

Characterising the drivers of tropical freshwater fish dynamics and abundance in the Mekong river, under environmental change

The Mekong river’s monsoon driven annual flood pulse creates a range of diverse habitats, with high levels of connectivity and primary productivity that support and trigger fish migratory dynamics and abundance. This abundance is reflected in the fact that the Mekong is the World’s most productive inland fisheries, supporting between 2.8-3.2 million tonnes of catch annually, underpinning the food security of over 70 million people.This thesis explores the impacts of climate change and anthropogenic activity on Mekong hydrology and system function, and the impacts these have on fish and fisheries. It combines an interdisciplinary approach utilising earth observation, historical fisheries data and hydrological records, alongside the application of hydrological modelling tools and the testing of new environmental DNA metabarcoding analyses, in order to explore how changes in Mekong hydrology will affect fish populations into the future.The results highlight a range of projected negative impacts of hydropower development, irrigation expansion and climate change on the dai fisheryresources, and in turn a range of significant impacts on regional fish protein availability, which primarily result from the blockage of key migratory routes caused by dam construction as well as changes in the timing of the flood pulse in key areas in the basin such as Tonle Sap Great Lake. The findings in this study urge a need to prioritise environmental conservation action centred on a need to maintain the historical flood pulse hydrologic regime of the Mekong river. Such a pulse is shown to be important in sustaining floodplain flood dynamics and habitat connectivity that maintains the critical dai fishery, enables migratory fish dynamics, and is thus key to overall regional food security