A genetic algorithm for tributary selection with consideration of multiple factors

Drainage systems are important components in cartography and Geographic Information Systems (GIS), and achieve different drainage patterns based on the form and texture of their network of stream channels and tributaries due to local topography and subsurface geology. The drainage pattern can reflect the geographical characteristics of a river network to a certain extent. To preserve the drainage pattern during the generalization process, this article proposes a solution to deal with many factors, such as the tributary length and the order in river tributary selection. This leads to a multi-objective optimization problem solved with a Genetic Algorithm. In the multi-objective model, different weights are used to aggregate all objective functions into a fitness function. The method is applied on a case study to evaluate the importance of each factor for different types of drainage and results are compared with a manually generalized network. The result can be controlled by assigning different weights to the factors. From this work, different weight settings according to drainage patterns are proposed for the river network generalization

Optimisation of connections to a fibre network

Stronger competition together with the development of new technologies have forced the Telecom Service Providers (TSP's) in the Netherlands to look for sophisticated optimisation methods to reduce the costs of their communication services especially for new areas such as the application of fibre technology.Fibre is being considered as the transmission medium of the future because fibre deadens the signals much less than the traditional media such as copper and coax, a lot of data can be transmitted at the same time and there are only a few failures. Another advantage is that fibre cables are thin and light so that they can be put into the ground rather easily.This article describes optimisation models with the objective to minimise the costs of constructing and managing a fibre network.The optimisation models have been developed to support decisions about the design and use of a fibre network and are based on the practical situation at Enertel being one of the new TSP’s. For Enertel a national backbone was already realised. The main problem to be solved concerned the optimisation of the access to the fibre network.

Diversification Across a Dynamic Landscape: Phylogeography and Riverscape Genetics of Speckled Dace (Rhinichthys osculus) in Western North America

Evolution occurs at various spatial and temporal scales. For example, speciation may occur in historic time, whereas localized adaptation is more contemporary. Each is required to identify and manage biodiversity. However, the relative abundance of Speckled Dace (Rhinichthys osculus), a small cyprinid fish in western North America (WNA) and the study species for this dissertation, establishes it an atypical conservation target, particularly when contrasted with the profusion of narrowly endemic forms it displays. Yet, the juxtaposition of ubiquity versus endemism provides an ideal model against which to test hypotheses regarding the geomorphic evolution of WNA. More specifically, it also allows the evolutionary history of Speckled Dace to be contrasted at multiple spatial and temporal scales, and interpreted in the context of contemporary anthropogenic pressures and climatic uncertainty. Chapter II dissects the broad distribution of Speckled Dace and quantifies how its evolution has been driven by hybridization/ introgression. Chapter III narrows the geographic focus by interpreting Speckled Dace distribution within two markedly different watersheds: The Colorado River and the Great Basin. The former is a broad riverine habitat whereas the latter is an endorheic basin. Two biogeographic models compare and contrast the tempo and mode of evolution within these geologically disparate habitats. Chapter IV employs a molecular clock to determine origin of Speckled Dace lineages in Death Valley (CA/NV), and to contrast these against estimates for a second endemic species, Devil’s Hole Pupfish (Cyprinodon diabolis). While palaeohydrology served to diversify Rhinichthys, its among-population connectivity occurred contemporaneously. These data also provide guidance for assessing the origin of the Devil’s Hole Pupfish, a topic of considerable contention. The final two chapters present bioinformatic software that facilitates the analysis of single-nucleotide-polymorphism (SNP) DNA data (used herein). Chapter V describes COMP-D, a program designed to assess introgression among lineages, whereas Chapter VI presents programmatic modifications to BAYESASS that allow migration to be quantified from SNP datasets. These five studies provide an in-depth understanding of contemporary and historical processes that shape aquatic biodiversity in environments prone to anthropogenic disturbance. They also highlight the complexities of evolutionary mechanisms and their implications for conservation in a changing world

Beyond Biomass: Valuing Genetic Diversity in Natural Resource Management

Strategies for increasing production of goods from working and natural systems have raised concerns that the diversity of species on which these services depend may be eroding. This loss of natural capital threatens to homogenize global food supplies and compromise the stability of human welfare. We assess the trade off between artificial augmentation of biomass and degradation of biodiversity underlying a populations' ability to adapt to shocks. Our application involves the augmentation of wild stocks of salmon. Practices in this system have generated warnings that genetic erosion may lead to a loss of the “portfolio effect” and the value of this loss is not accounted for in decision making. We construct an integrated bioeconomic model of salmon biomass and genetic diversity. Our results show how practices that homogenize natural systems can still generate positive returns. However, the substitution of more physical capital and labor for natural capital must be maintained for gains to persist, weakens the capacity for adaptation should this investment cease, and can cause substantial loss of population wildness. We apply an emerging optimization method—approximate dynamic programming—to solve the model without simplifying restrictions imposed previously

BROOK TROUT SALVELINUS FONTINALIS DISTRIBUTION, GENETIC DIVERSITY, AND HABITAT USE IN AN ADIRONDACK RIVER SYSTEM, NEW YORK

This study examined population dynamics, ecology, genetic diversity, and habitat use of wild Brook Trout in tributaries of the East Branch Ausable River, NY from headwaters to mouth. Brook Trout population abundance was estimated and fish community composition was documented along the longitudinal gradient of the East Branch Ausable River. Brook Trout were found throughout this watershed, and multivariate analysis demonstrates that habitat variables influence community assemblage. In addition to elevation, gradients of forest cover, temperature, and percent impervious surfaces explained variation of fish distribution in this watershed. Population genetic analyses demonstrated that natural reproduction of wild and hatchery fish is occurring in the headwaters. Brook Trout in the headwaters of the Ausable River are an admixed population of wild and domestic-Temiscamie fish, and results show lasting effects of fish stocking on the genetic diversity and population status of this system

A comparative study of marriage in honey bees optimisation (MBO) algorithm in multi-reservoir system optimisation

Contemporary reservoir systems often require operators to meet a variety of goals and objectives; these in turn frequently complicate water management decision-making. In addition, many reservoir objectives have non-linear relationships and are therefore difficult to implement using traditional optimisation techniques. A practical application of the marriage in honey bees optimisation (MBO) algorithm is being utilised for Karkheh multi-reservoir system, south-western Iran, where supplying irrigation water for agricultural areas and maintaining a minimum in-stream flow for environmental purposes is desired. Optimal monthly reservoir release information by MBO is highlighted and the results compared to those of other evolutionary algorithms, such as the genetic algorithm (GA), ant colony optimisation for continuous domains (ACOR), particle swarm optimisation (PSO) and elitist-mutation particle swarm optimisation (EMPSO). The results indicate the superiority of MBO over the algorithms tested.Keywords: non-linear optimisation, multi reservoir system, honey bee mating optimisation algorithm, evolutionary algorithms, meta-heuristic algorithm

Using QUAL2Kw as a Decision Support Tool: Considerations for Data Collection, Calibration, and Numeric Nutrient Criteria

The in-stream water quality model, QUAL2Kw, can provide guidance in watershed management decisions by linking changes in nutrient loads to responses in water quality. This model is particularly useful for determining wasteload allocations, aiding in total maximum daily load analyses, and developing numeric nutrient criteria. Unfortunately, states struggle to balance the data collection and modeling requirements to accomplish many of these water quality management tasks due to limited resources. This commonly results in routine data collection and monitoring efforts that do not satisfy the data requirements for modeling. To address this disconnect, this study presents a data collection and parameter calibration methodology suited to meet general QUAL2Kw modeling requirements. Then, with the goal of identifying a range of numeric nitrogen and phosphorus criteria, this general data collection and modeling strategy was applied to sites throughout Utah. To help automate and test scenarios targeted at tracking effects of loading and response combinations, a nutrient criteria tool was also developed to interface with these QUAL2Kw models. By implementing the tool on these models, input concentrations of ammonium (NH4+) ranging from 10 to 101 µg/L and inorganic phosphorus (PO4-) ranging from 1 to 14 µg/L were found to exceed thresholds of bottom algae, gross primary productivity, and ecosystem respiration. Conversely, NH4+ concentrations above 3,500 µg/L and PO4- above 490 µg/L exceeded dissolved oxygen thresholds of 5-6 mg/L in some applications. Some limitations of using mechanistic models in this manner were identified, including model capabilities (e.g., steady-state versus dynamic), inclusion of appropriate processes, uncertainty in calibrated parameters, and site-specific conditions. Although many problems will require more complex modeling efforts with significantly larger data collection efforts, this approach provides an initial framework that aids in the judicial use of resources to aid in watershed management decisions

Genetic population structure of the monogenean parasite Gyrodactylus thymalli and its host European grayling (Thymallus thymallus) in a large Norwegian lake

Understanding how populations are structured in space and time is a central question in evolutionary biology. Parasites and their hosts are assumed to evolve together, however, detailed understanding of mechanisms leading to genetic structuring of parasites and their hosts are lacking. As a parasite depends on its host, studying the genetic structure of both parasite and host can reveal important insights into these mechanisms. Here, genetic structure of the monogenean parasite Gyrodactylus thymalli and its host the European grayling (Thymallus thymallus) was investigated in 10 tributaries draining into the large Lake Mjøsa in Norway. The population genetic structure of spawning grayling was studied using microsatellite genotyping, while G. thymalli was studied by sequencing a mitochondrial DNA gene (dehydrogenase subunit 5). Two main genetic clusters were revealed in grayling, one cluster comprising grayling from the largest spawning population, while the remaining tributaries formed the second cluster. For both taxa, some genetic differentiation was observed among tributaries, but there was no clear isolation-by-distance signature. The structuring was stronger for the host than for the parasite. These results imply that moderate to high levels of gene flow occur among the sub-populations of both taxa. The high parasite exchange among tributaries could result from a lack of strong homing behavior in grayling as well as interactions among individual fish outside of the spawning season, leading to frequent mixing of both host and parasite.publishedVersio

Prioritizing Mitigation of Road-Stream Crossings for Resident Aquatic Organisms by Accounting for Habitat Quantity, Quality, and Accessibility

Road crossings and dams may act as barriers to movement for a wide range of aquatic organisms in lotic freshwater systems. Limited funding constrains the number of barriers that may be mitigated by repair or removal, so systematic methods of prioritization are needed for selecting barriers for mitigation. A new formulation is proposed that links the number of organisms in the watershed to the amount and quality of accessible habitat in order to quantify habitat connectivity of a watershed. The method is applied to a case study performed on the Upper West Branch of the Westfield River in Massachusetts, with multispecies measures of habitat integrity and aquatic barrier passability allowing comparison of stream segments and barriers within the network and their contributions to overall habitat availability. Optimization techniques are used to maximize the amount of high-quality habitat in the network accessible by stream-resident organisms. Results of this study demonstrate that the optimal combination of barriers for mitigation may change dramatically as budgets change, and that foreknowledge of a project’s lifetime budget and accurate data regarding mitigation costs for individual barriers are crucial to cost-effective barrier removal planning

The roles of history, geography, and environment in shaping landscape genetic variation and its applied significance

The decline and loss of species and genetic diversity as a result of anthropogenic change is occurring at an unprecedented rate, reshaping biodiversity and restructuring ecosystems. Population genetic variation is shaped by evolutionary processes and in turn determines the evolutionary potential of natural populations. Facilitated by recent improvements in DNA sequencing technologies, population genomic analyses can resolve patterns of genetic differentiation and evolutionary history, characterize the effects of evolutionary process on genome variation, and facilitate an understanding of how response to environmental variation may underlie local adaptation. Such analyses can inform conservation and restoration by establishing baseline patterns of genetic variation across the landscape, recognizing evolutionary significant units, sourcing propagules for restoration, and predicting species response to changing environmental conditions. Here, I applied high throughput DNA sequencing approaches to characterize the historical, spatial, and environmental factors shaping genetic variation in several systems of conservation and restoration significance. First, I investigated hierarchical genetic structure and evolutionary history of Hucho taimen (taimen, the world’s largest salmonid), listed as vulnerable by the International Union for Conservation of Nature (IUCN), across multiple river basins in Russia and Mongolia. Second, I characterized patterns of emergent population genetic structure of nonnative Oncorhynchus mykiss (rainbow trout) in the Lake Tahoe basin to inform reintroduction of the U.S. Endangered Species Act listed native cutthroat trout Oncorhynchus clarkii henshawi (Lahontan cutthroat trout). Rainbow trout have been widely introduced across the globe, stocked for >50 years into Lake Tahoe, and an understanding of population genetic structure may help inform strategies for successful native species reintroduction. Finally, I quantified spatial genetic structure, identified environmental variables potentially involved in local adaptation, and predicted variation in maladaptation under projected climate change across the range of Pinus muricata, a closed-cone pine occurring in a small number of isolated and disjunct stands along the coast of California, and also listed as vulnerable by the IUCN. Collectively, my research highlights the wide utility of population genomic analyses for taxa of conservation and restoration significance