Coal surface mining and associated reclamation practices have had an immense impact on the landscape of the Appalachian region of the United States. However, their effect on floral and faunal conservation has been poorly documented. Lepidopteran communities, vegetation, and nectar resources were studied on 19 mine sites reclaimed 0-30 years previously and five sites in the surrounding hardwoods in southwestern Virginia. The goals of this work were to characterize vegetational and lepidopteran communities of these sites; to understand the relationships between the two; and to assess the role of mine reclamation in regional conservation efforts. Vegetational community composition of the reclaimed sites appeared to be approaching that of the hardwood sites as time since reclamation increased. However, it will take a number of years, if ever, before the vegetational community composition and structure approximate that of the hardwoods. Between-site variation in vegetational communities was greater in the hardwoods, than the reclaimed sites. Recently reclaimed mined sites hosted a large number of both individuals and species of diurnal lepidoptera, comprising mostly widespread, generalist species. Multivariate analysis suggested that lepidopteran community composition of reclaimed sites was approaching that of the hardwoods and that lepidopteran communities of later successional reclaimed sites were fairly similar to those of the surrounding hardwoods. Moth community composition closely reflected vegetational community composition and species richness, while butterflies were poor indicators of vegetational communities. Reclaimed sites provided much more abundant and diverse nectar resources than hardwood forests. Results of nectar studies and butterfly behavioral observations suggested that adult butterfly community composition was strongly influenced by nectar abundance, but that nectar was not a limiting resource. While reclaimed sites hosted a number of the more common plant and lepidopteran species, it remains questionable whether reclaimed areas will ever host the entire complement of the biota present prior to disturbance. In order to further conservation efforts, rehabilitation projects must be designed and monitored over larger spatial and longer temporal scales. / Ph. D.

Thesis (MScAgric (Conservation Ecology and Entomology)--University of Stellenbosch, 2005. / A semi-arid country, like South Africa, with unpredictable seasonal rainfall, is subject to great scarcity in water and an ever-increasing demand from the rising human population. Therefore, efficient reservoirs as well as monitoring methods are needed to manage the South African water supply. This study was undertaken on the Eerste River in the Western Cape, South Africa, focusing on the impact of the Klein Plaas dam system on the benthic macroinvertebrates. The study also examined the use of benthic macroinvertebrates as bioindicators of water quality with special reference to the South African Scoring System Version 5(SASS5) that is currently being used nationally. The impoundment of the water, as well as the inter-basin transfer programme and the experimental cage-culture trout farm, all play a significant role in the disturbance impact of the dam on the Eerste River system. The disturbance is manifested as a drop in water quality that can be seen in the distribution of keystone species, changes in the riparian vegetation, as well as in physical-, chemical-, and biomonitoring evaluations. The study also indicated that the SASS5 is effective, but needs some adjustments, such as inclusion of a prediction phase, finer spatial-scale methodologies and greater consideration of the rarity of species.

Thesis (MSc)--University of Stellenbosch, 2005. / ENGLISH ABSTRACT: Invasive alien trees, especially Acacia species, are a great threat to biodiversity in South African rivers. The national Working for Water Programme is addressing the alien problem by removing alien trees from river margins. The concern is that this may be creating even further disturbance by affecting water quality and habitats. In particular, how is this affecting rare and endemic species? Benthic macro invertebrates and aerial odonates were assessed along five Western Cape rivers in alien-invaded, cleared and natural sites between December and March. The aim was to assess the effect of both alien invasion and alien clearing on aquatic invertebrates. Odonata, being easily sampled, were also assessed as they are severely affected by the lack of understorey plants in shaded, alien-invaded sites. Odonata and benthic macroinvertebrates were treated as two separate studies and no attempt was made to correlate the results obtained from both studies. SASS5, a qualitative, rapid bioassessment technique, based on the sensitivity of the families present, was used as a measure of river health and, indirectly, of water quality. SASS indicated a decline in water quality conditions after alien clearing, a likely response to the greater insolation as well as erosion of cleared banks, resulting in elevated temperatures and suspended solids and lowered oxygen levels. Community responses to alien disturbance and other environmental factors were analysed using PRIMER and CANOCO software. Assemblages of Odonata were found to provide a rapid, cost-effective means of assessment and monitoring. Potential indicator and detector species were also identified using the lndicator Value method. Assemblage patterns of aquatic invertebrates, however, were dominated by between-river and seasonal effects. Therefore, while SASS detected overall changes in river health, without identifying the cause, potential aquatic detector taxa were identified that may be useful for linking general disturbance to alien invasion or clearing. All indicator and detector taxa identified in both studies can be used for long-term monitoring and for identifying biodiverse areas for clearing or protection. In both studies, sensitive, endemic taxa were lost after clearing, being replaced by more tolerant, widespread taxa. Recovery of the biota appears to follow the recovery succession of the vegetation, with most sensitive or endemic taxa only appearing after the recovery of indigenous plants. A number of recommendations are made regarding the restoration of both water quality (particularly with respect to shade and soil erosion) and biotope availability (particularly in terms of the recultivation of indigenous plants) in order to achieve biodiversity objectives. The role of catchment management, prioritisation procedures and long-term monitoring are also discussed. / AFRIKAANSE OPSOMMING: Uitheemse, indringerbome, veral Acacia spesies, is 'n groot bedreiging vir biodiversiteit in Suid- Afrikaanse riviere. Die nasionale Werk vir Water-projek spreek hierdie probleem aan deur uitheemse bome van rivieroewers te verwyder. Die kommer is dat water kwaliteit en habitatte sodoende verder versteur kan word. Byvoorbeeld, hoe word endemiese en bedreigde spesies geraak? Akwatiese makroinvertebrate en volwasse Odonata in vyf Wes-Kaapse riviere is tussen Desember en Maart bestudeer en gemonster in natuurlike gebiede, in gebiede waar indringerbome teenwoordig is, en in gebiede waar hulle verwyder is. Die doel was om die effek van indringerverwante impakte op akwatiese invertebrate vas te stel. Odonata is ook bestudeer omdat hulle maklik gemonster kan word en omdat hulle ernstig geraak word deur indringers. Die uitheemse plantegroei oorskadu die oewers en verhoed die groei van inheemse oewerplante. Die bentiese makro-invertebrate en Odonata is as twee aparte studies behandel en geen poging is gemaak om die resultate van die twee te vergelyk nie. SASSS, 'n kwalitatiewe, bioasseseringsmetode wat op die sensitiwiteit van die aanwesige families baseer word, is gebruik om waterkwaliteit op 'n indirekte manier te bepaal. SASS het aangedui dat daar 'n afname in waterkwaliteit is nadat indringerplante verwyder is. Dit is moontlik as 'n gevolg van groter blootstelling aan sonskyn en erosie van rivieroewers wat veroorsaak dat temperature en die hoeveelheid gesuspendeerde materiaal verhoog word, en dat suurstof konsentrasies verminder word. Die gevolge van indringerplante en ander omgewingsfaktore op akwatiese gemeenskappe is met PRlMER en CANOCO sagteware ontleed. Groepering van Odonata kan gebruik word om op 'n maklike en koste-effektiewe manier om die impak van indringerplante en hul verwydering te bepaal en te monitor. Aanwyserspesies is ook deur middel van die 'Indicator Value' metode geïdentifiseer. Die verspreidingspatrone van invertebraatspesies word deur geografiese en seisoenale effekte oorheers. Dus, terwyl SASS veranderinge in waterkwaliteit kan aantoon, sonder om die oorsaak daarvan te identifiseer, kan aanwyserspesies gebruik word om meer spesifieke impakte deur indringerplantegroei, of indringerverwydering, te bepaal en te monitor. Hulle kan ook gebruik word om gebiede met hoë biodiversiteit vir bewaring of indringerverwydering te identifiseer. Beide studies dui aan dat sensitiewe en endemiese taksa na indringerverwydering verlore gaan, en vervang word met meer geharde, wydverspreide taksa. Herstel van die biota volg op die herstel van die plant gemeenskappe, en die mees sensitiewe of endemiese taksa herstel eers nadat die inheemse plantegroei herstel het. 'n Aantal aanbevelings in verband met die restorasie van waterkwaliteit (veral in terme van die hoeveelheid skaduwee en erosie) en die beskikbaarheid van biotope (veral in terme van inheemse plante) om biodiversiteitsdoelwitte te bereik word gemaak. Die rol van opvanggebied bestuur, voorrang prosedures en lang termyn monitering word ook bespreek.

The fish community structure of two contrasting estuaries, one with a well developed mangrove forest (Mngazana) and the other without mangroves (Mngazi) was compared. Both the Mngazi and Mngazana estuary fish communities were dominated by marine species, reflecting the importance of these systems as nursery areas for marine fishes. The Mngazi Estuary contained 18% more estuarine fishes in terms of catch per unit effort (CPUE) than the Mngazana Estuary. The reduced tidal influence due to the narrow mouth opening is a possible reason for the heightened CPUE of estuarine species in the Mngazi estuary. The recorded higher diversity of fish species in the Mngazana Estuary when compared with the Mngazi Estuary was attributed to the greater influence of the marine environment due to the wide permanently open mouth, as well as the presence of a variety of habitats in this system. In both estuaries tropical and temperate species were captured, confirming the transitional nature of their biogeographic location which is situated close to the boundary between the subtropical and warm temperate regions of the Southern African coastline. Contrary to previous studies, which recorded seasonal changes in the proportions of tropical and temperate species, the proportions of tropical species remained unchanged at approximately 70% during the January and June sampling occasions. Global warming as a possible reason for the increased dominance of tropical species is discussed. Although several studies in southern Africa have investigated estuarine food web structure, none have compared mangrove and non-mangrove estuaries. In this study, the primary sources of carbon utilised by the fish fauna in the Mngazi and Mngazana estuaries was investigated. The carbon isotopic values of fishes in both estuaries displayed a continuum rather than a tight clustering around particular energy sources. Most detritus feeders of the family Mugilidae (mullets) from both estuaries were relatively more enriched than other fish taxa. The isotopic values of the mullet species suggest a diet derived from relatively enriched carbon sources such as benthic microalgae, the eelgrass Zostera capensis and associated epiphytes. Based on the isotopic values, piscivorous fishes from both estuaries could not be linked to specific prey fish taxa, but clearly the mullet species were not their main food source. The invertebrate feeders that were found in both estuaries showed greater isotopic variations in the Mngazana Estuary than in the Mngazi Estuary, probably reflecting the higher diversity of habitats (carbon sources) and invertebrate prey species in the Mngazana system. Generally the isotopic signatures of fishes from the Mngazi Estuary were more enriched than those from the Mngazana Estuary, thus indicating the possible effect of δ¹³C depleted mangrove derived carbon in the latter system.

The historical range of the Indus River dolphin has declined by 80% since the 19th century and has been fragmented into 17 river sections by construction of irrigation barrages. Dolphin sighting and interview surveys showed that river dolphins persist in six river sections, have been extirpated from ten, and are of unknown status in the remaining section. Logistic regression and survival modelling showed that low dry season river discharge was the primary factor responsible for the Indus dolphins range decline. Abundance of the three largest Indus dolphin subpopulations was estimated using tandem vessel-based direct counts, corrected for missed animals using conditional likelihood capture-recapture models. The entire subspecies was estimated to number between 1550-1750 in 2006. Dolphin encounter rates within the Guddu-Sukkur subpopulation (10.35/km) were the highest reported for any river dolphin and direct counts suggest that this subpopulation may have been increasing in abundance since the 1970s when hunting was banned. The dry season habitat selection of Indus dolphins was explored using Generalised Linear Models of dolphin distribution and abundance in relation to river geomorphology, and channel geometry in cross-section. Channel cross-sectional area was shown to be the most important factor determining dolphin presence. Indus dolphins avoided channels with small cross-sectional area <700m2, presumably due to the risk of entrapment and reduced foraging opportunities. The phylogenetics of Indus and Ganges River dolphins was explored using Mitochondrial control region sequences. Genetic diversity was low, and all 20 Indus River dolphin samples were identical. There were no haplotypes shared by Indus and Ganges River dolphins, phylogenetic trees demonstrated reciprocal monophyletic separation and Bayesian modelling suggested that the two dolphin populations diverged approximately 0.66 million years ago. Declining river flows threaten Indus dolphins especially at the upstream end of their range, and it is important to determine how much water is required to sustain a dolphin population through the dry season. Fisheries interactions are an increasing problem that will be best addressed through localised, community-based conservation activities.

Conservation of intertidal habitats in the UK is vital in order to continue to support nationally and internationally important populations of non-breeding waterbirds. Historic reclamation for agriculture and industry has resulted in the loss and degradation of large areas of these intertidal habitats in estuaries and they continue to be threatened by sea-level rise. Managed realignment is one method which is increasingly being used to restore intertidal habitats. As managed realignment is a relatively new restoration technique, the extent to which knowledge of the biology of estuaries is applicable to managed realignment sites is unclear. Habitat restoration is often unsuccessful or incomplete, so a detailed knowledge of both the natural system and the characteristics of restored systems will usually be necessary to recreate fully-functional estuarine habitats. This thesis focuses on Nigg Bay Managed Realignment Site (Nigg Bay MRS), the first managed realignment site in Scotland, and follows the first four years of ecological development to gain an understanding of how breached realignment can be used to restore intertidal habitats to support non-breeding waterbirds. This thesis has six major aims: (i) to describe the development of saltmarsh, (ii) to describe the development of intertidal flat, (iii) to describe the colonisation by non-breeding waterbirds (iv) to determine how tidal cycle and weather affect patterns of waterbird use, (v) to determine which factors affect the spatial distribution of waders and finally (vi) to determine the patterns of use by individual birds. Four summers after the re-establishment of tidal conditions, almost all of the saltmarsh species recorded on the nearby saltmarsh had colonised Nigg Bay MRS, although recognisable communities had yet to establish. Three winters after the re- establishment of tidal conditions in Nigg Bay MRS, the sediments had a significantly smaller particle size and higher organic matter content compared to the fine sands of the adjacent intertidal flats. The intertidal invertebrate community also differed from the adjacent intertidal flats. Nigg Bay MRS attracted large numbers of non-breeding waterbirds and supported each of the most common wader and wildfowl species present in the wider estuary. Nigg Bay MRS performs a number of important functions for non-breeding waterbirds by: (i) providing a foraging and resting habitat when the tide is absent and intertidal sediments in Nigg Bay are exposed; (ii) providing a foraging resource as the tide passes over the intertidal sediments within the site once the intertidal flats in Nigg Bay are inundated; and (iii) providing a high tide roosting site. On days with low temperatures and high wind speeds, more waterbirds use Nigg Bay MRS, suggesting that it is likely to be providing sheltering benefits. Nigg Bay MRS also provides top-up feeding habitat. The factors that often influence the spatial distributions of waders in estuaries appear to be operating within Nigg Bay MRS. Wader densities are greater on the intertidal flats when they are accessible than on the saltmarsh. Wader densities are also greatest close to creeks and drainage channels, possibly due to higher invertebrate densities, more accessible prey or sheltering benefits. Colour-ringing and radio-tracking of Common Redshank established that Nigg Bay MRS has a subset of regular users, including both adults and juveniles, and the wader assemblage at night may differ from the assemblage during the day. These findings are discussed in terms of the implications for locating, designing and managing future managed realignment projects.

This study was an investigation of lotic macroinvertebrate distribution in northeastern Oregon at two different spatial and biological scales. Examination of assemblages at a limited spatial scale revealed relationships with natural and disturbance gradients and led to questions about distribution of a population at broader spatial scales. In a 16 kilometer section of the North Fork John Day River, I examined the relationship of invertebrate assemblages to habitat and fine sediment deposition. This river section was subjected to sediment inputs resulting from several years of floodplain mine-tailing leveling, and erosion and tributary channel scouring following a forest fire. Invertebrate assemblages differed between habitat types. The proportion of sediment tolerant invertebrates, especially oligochaete worms, increased with higher amounts of deposited fine sediment, but total invertebrate abundance was not related to deposited sediment. The response of sediment tolerant invertebrates appeared to reflect cumulative impacts from multiple input points and downstream transport of sediment and cumulative and/or increasing impacts over the two years of sampling. In studying assemblages in the North Fork, I noticed an unusual abundance of the caddisfly, Lopidostoma pluviale (Milne). In a more spatially extensive examination of a population, I investigated distribution of this caddisfly in the Blue Mountain region of northeastern Oregon. L. pluviale was more common and/or abundant further downstream than would be expected for a shredding feeder based on the River Continuum Concept (Vannote, et al., 1980). Through gut content analyses, I demonstrated that this species is much more of a generalist feeder than its designation as a shredder would imply. Consequently, its distribution is not limited to headwaters where allochthonous food resources are abundant. I hypothesize that non-food environmental factors may be more important in determining the distribution of this species. Results of this research indicate that assemblage studies can reveal interesting relationships with environmental conditions. In addition, paying attention to unusual distributions of taxa in assemblage studies can lead to further studies that can improve our understanding of the biology and ecology of species. / Graduation date: 2004

Debris flows, common disturbances in many mountainous areas, initially scour or bury stream habitats; however, debris flows deliver vast amounts of wood, boulders, and gravel that may ultimately form complex stream habitat to potentially support a diverse salmonid assemblage. The materials deposited by debris flows would otherwise be inaccessible to streams, and thus deposits may play an important role in creating and maintaining complex salmonid habitat over time. Despite the potential of deposits for increasing habitat complexity, most fish studies have focused on the destructive effects of debris flows and short-term recovery and re-colonization in scour zones. Debris-flows that occurred during the record-setting winter storms of 1996 in western Oregon, USA, provide an opportunity to study intermediate-term effects of debris-flow deposits on abundances and habitat for juvenile salmonids. In this setting, I surveyed salmonid abundance and habitat in three Oregon Coast Range streams that contained several debris-flow deposits from the 1996 storms. I explained fish abundance using hierarchical models, accounting for heterogeneous detection probabilities with repeated counts from multiple-pass snorkeling. The "best" hierarchical model of detection probability and abundance was selected (QAIC) from pool and snorkel-pass characteristics separately for juvenile coho salmon (Oncorhynchus kisutch), age 0+ trout, and age 1+ trout (Oncorhynchus spp.) in each stream. Adding distance to the nearest 1996 debris-flow deposit (DDF) produced a significant drop-in-deviance for four of nine "best" models, including at least one in each stream and for each species/age-class. In these four models, salmonid abundance decreased with increasing distance from deposit. As a potential explanation, several pool habitat characteristics were correlated (Spearman's rank) with DDF. Results varied across streams, but generally, percent of substrate as bedrock was lower and boulder density and percent substrate as gravel were higher closer to deposits. Although repeat counts are increasingly used in hierarchical modeling of heterogeneous detection probabilities and abundance for other wildlife species, studies of fish often rely on uncalibrated, single-pass snorkel counts. When exploring the value of repeat counts, I found that juvenile salmonid abundance decreased with increasing distance from debris-flow deposits in more multiple-pass hierarchical models that accounted for heterogeneous detection probabilities than for single-pass models that did not. Thus, modeling heterogeneous detection probabilities with repeated snorkel counts may be beneficial in other situations, addressing limitations of uncalibrated indices without relying on methods such as electrofishing, which may be difficult or impossible for remote study areas, longer surveys, or sensitive species. My findings suggest that debris-flow deposits may influence salmonid abundances after 15 years, and support management of debris flow-prone hillslopes and low-order channels to deliver elements of stream habitat complexity. / Graduation date: 2013

Eighteen prairie rattlesnakes (Crotalus viridis viridis) were tracked using radio-telemetry and 82 snakes were PIT-tagged over a 2-year period in Lethbridge, AB to determine population size, movement patterns, and habitat utilization, and to predict fragmentation effects on the species within an urban locale. Population size was estimated using closed population models at 374 snakes (295 adults) and open population models at 204 snakes (161 adults), greater than an estimate of <50 adults in 2003 (Ernst, 2003) and 2006 (Ernst & Quinlan, 2006). Mean home range sizes, based on 95% minimum convex polygon analysis, differed significantly between years (31.51 ha in 2005, 3.72 ha in 2006). Calculated movement parameters, such as mean distance moved per day, total distance moved over the course of the active season, and frequency of movement varied between years and individuals. Greater-than-expected (under hypotheses of even habitat choice) utilization was observed in habitat types located within coulee and flood plain areas, with apparent preference towards unbroken parcels of grassland or cottonwoods, whereas less-than-predicted utilization of agricultural habitat type was observed. Fragmentation effects on prairie rattlesnake movement and occurrence were examined through modeling and were found to coincide with observed species’ locations, suggesting that prairie rattlesnakes are undergoing modification of movement patterns to avoid highly concentrated human density or use. Influence of weather on the use of vegetative ground cover was observed, as it was accessed more by prairie rattlesnakes at higher temperatures. Recommendations towards future management of the prairie rattlesnake population in Lethbridge are given, including protection of the Bridge View Drive site and inclusion of varied habitat types and terrain when planning habitat and wildlife corridors. Management decisions that ensure remaining habitat parcels and connective areas near rattlesnake foraging or movement corridors are also advocated. Identification of future research focuses include studies on juvenile survivorship, genetic structure, and vehicle-related mortality. / xii, 83 leaves : col. ill., col. maps ; 29 cm

Cattle grazing in riparian zones can have large impacts on vegetation characteristics and avian biodiversity. To assess these impacts in southern Alberta, vegetation and bird surveys were conducted in twelve riparian sites (four each in heavily grazed, moderately grazed, and ungrazed habitats) along the Oldman River. The shrub understory and bird species diversity and abundance declined significantly as grazing intensity increased. Settlement patterns, territory sizes, and food provisioning rates of some bird species were examined to assess the mechanisms behind this reduction. Five out of seven species settled earlier in ungrazed habitats, whereas two species did not show any discernable settlement pattern. The territory sizes of three species examined increased as grazing intensity increased. House wrens (Troglodytes aedon) brought more food and more food biomass to their nests in ungrazed habitats. These results indicate that available food biomass decreased as grazing intensity increased, and is an important factor in population dynamics of some species. / 29 cm.