Browsing by Subject "Connectivity"

This dissertation focuses on the implications of habitat change in freshwater ecosystems. Habitat change has three primary components that are inextricably connected; habitat loss, alteration, and fragmentation. Habitat loss is the physical removal and/or replacement of “core” habitat such that a new “matrix” habitat exists in its place. Habitat alteration is the modification of core habitat that causes a quality change (either positive or negative depending on the target species). Habitat fragmentation affects the connectivity between core habitat patches in the landscape. Rivers are highly fragmented both naturally and anthropogenically, so they represent a system readily available to study the impacts of habitat change on ecosystems.

Four approaches were used to evaluate the impacts of habitat change on freshwater ecosystems. First (Chapter 1 as published in the Annals of the New York Academy of Sciences with co-authors Dr. Martin Doyle and Dr. David Strayer; see Fuller et al. (2015)), a review of the major causes and consequences of habitat change in river networks was conducted with the goal of also bridging a theoretical gap between terrestrial and freshwater systems related to habitat change ecology. Second (Chapter 2), an empirical evaluation of a fragmented (dammed) river reach was used to evaluate the local impacts of habitat loss and alteration on physical (sediment), biogeochemical (dissolved oxygen), and biological (freshwater mussels) response variables. Third (Chapter 3), gene flow model simulations were used to identify the genetic impacts of habitat fragmentation at the river-network scale. This simulation effort contrasted the impact of habitat fragmentation with species longevity to see how organisms using different life history strategies related to lifespan respond genetically to habitat fragmentation. Fourth (Chapter 4), an empirical landscape genomics evaluation of a species of freshwater mussel (Elliptio complanata) was conducted to identify its genetic response to a river network with a long history of habitat change.

Conclusions from this research make several contributions to the ecological theory of habitat change. First, by applying the habitat change lexicon in terrestrial systems to freshwater systems, sharing results and theory across the terrestrial-aquatic literature becomes simple and may advance the theory behind habitat change ecology more rapidly with more empirical results to draw upon. Second, temporally dynamic matrix habitat and species capitalizing on altered edge habitat were identified surrounding a local habitat fragmentation agent (a dam), suggesting some species may strongly benefit from the presence of edge habitat in river networks. Third, from the gene flow model simulations, the life history of a species played an important role in how organisms respond genetically to habitat fragmentation where long-lived species appear buffered from the genetic diversity loss caused by habitat fragmentation. Finally, the empirical evaluation of a freshwater mussel species that has experienced a long history of anthropogenic-driven habitat change via water quality alterations, inundation losses, and dam fragmentation appears to have maintained a population genetic structure unrelated to the expected habitat change in the system.

Diffusion tensor imaging (DTI) has emerged as a unique method to characterize brain tissue microstructure non-invasively. DTI typically provides the ability to study white matter structure with a standard voxel resolution of 8μL over imaging field-of-views of the extent of the human brain. As such, it has long been recognized as a promising tool not only in clinical research for the diagnostic and monitoring of white matter diseases, but also for investigating the fundamental biological principles underlying the organization of long and short-range cortical networks. However, the complexity of brain structure within an MRI voxel makes it difficult to dissociate the tissue origins of the measured anisotropy. The tensor characterization is a composite result of proton pools in different tissue and cell structures with diverse diffusion properties. As such, partial volume effects introduce a strong bias which can lead to spurious measurements, especially in regions with a complex tissue structure such as interdigitating crossing fibers or in convoluted cortical folds near the grey/white matter interface.

This dissertation focuses on the design and development of acquisition and image reconstruction strategies to improve the spatial resolution of diffusion imaging. After a brief review of the theory of diffusion MRI and of the basic principles of streamline tractography in the human brain, the main challenges to increasing the spatial resolution are discussed. A comprehensive characterization of artifacts due to motion and field inhomogeneities is provided and novel corrective methods are proposed to enable the acquisition of diffusion weighted data with 2D mulitslice imaging techniques with full brain coverage, increased SNR and high spatial resolutions of 1.25×1.25×1.25 mm3 within an acceptable scan time. The method is extended to a multishot k_{_z}-encoded 3D multislab spiral DTI and evaluated in normal human volunteers.

To demonstrate the increased SNR and enhanced resolution capability of the proposed methods and more generally to assess the value of high-spatial resolution in diffusion imaging, a study of cortical depth-dependence of fractional anisotropy was performed at an unprecedented in-vivo inplane resolution of 0.390×0.390μm2 and an investigation of the trade-offs between spatial resolution and cortical specificity was conducted within the connectome framework.

Genetic diversity, population structure, and connectivity influence interactions among communities and populations. At hydrothermal vents in the western pacific, population structure in vent-associated species could occur at spatial scales ranging from vent sites separated by a few hundred meters to oceanic basins separated by more than 3000 kilometers. The spatial scale of population structure has important conservation implications; species that are well-connected across large geographic regions are more resilient to natural and anthropogenic disturbance. This dissertation examines the genetic diversity, population structure, and connectivity of 3 vent-associated species in the western Pacific. It first presents results from the development of microsatellite primers for Ifremeria nautilei, a deep-sea vent associated snail, then uses mitochondrial COI sequences and a suite of microsatellite markers to examine the broader connectivity of three vent-associated species, Ifremeria nautilei, Chorocaris sp. 2, and Olgasolaris tollmanni, across three back-arc basins in the western Pacific.

Within Manus Basin, no significant genetic differentiation was detected in populations of Ifremeria nautilei (based on COI and microsatellite), Chorocaris sp. 2 (based on COI and microsatellite), or Olgasolaris tollmanni (based on COI). A previously documented low-abundance cryptic species, Chorocaris sp. 1, was detected from a single site, South Su (based on COI). The population of I. nautilei in Manus Basin was found to be significantly differentiated from a second population that appeared to be panmictic across North Fiji and Lau Basin (based on COI and microsatellites). Chorocaris sp. 2 was also found to be significantly differentiated between Manus and North Fiji Basin (based on COI). Both I. nautilei and Chorocaris sp. 2 showed signs of potential low-level migration between Manus and other southwestern Pacific basins. O. tollmanni was undifferentiated between Manus and Lau Basin (based on COI). It is likely that a variable impedance filter exists that limits the realized dispersal of some, but not all species between Manus Basin and other western Pacific back-arc basins. The presence of a variable filter has implications for the conservation and management of hydrothermal vents in Manus Basin, as it is unclear what effects sustained anthropogenic disturbance will have on isolated populations of I. nautilei and Chorocaris sp. 2.