The endangered northern long-eared bat (<i>Myotis septentrionalis</i>) has experienced severe population declines since the 2007 introduction of <i>Pseudogymnoascus destructans</i>, the fungal pathogen that causes white-nose syndrome (WNS). Due to continued mortality, failed recruitment, and range fragmentation, effective species conservation would benefit from local and regional research related to habitat selection and suitability, seasonal activity, and large-scale estimates of continued occupancy across the post-WNS landscape. In this dissertation, I explored maternity colony home range size and habitat selection, both coastal and interior seasonal activity patterns, habitat suitability, and species occupancy trends in the Mid-Atlantic and Northeastern United States. Research from the Coastal Plain of North Carolina, based on diurnal roost locations, revealed that core and peripheral home range estimates were large but comparable to areas of contiguous forest cover in other regions of the species' range. Prior to juvenile volancy, female northern long-eared bats selected red maple (<i>Acer rubrum</i>), water ash (<i>Fraxinus caroliniana</i>), and loblolly pine (<i>Pinus taeda</i>) as day-roosts, but then used sweetgum (<i>Liquidambar styraciflua</i>), swamp bay (<i>Persea palustris</i>), and water tupelo (<i>Nyssa aquatica</i>) after juvenile volancy. At the second-order spatial scale (i.e., home range within a region), roosting home ranges were associated with woody wetlands farther from anthropogenic development and open water. However, within the third-order scale (i.e., core home range within a periphery), northern long-eared bats selected woody wetlands adjacent to intact upland forests, areas containing shorter trees and occurring proximal to open water. Research utilizing passive acoustic monitoring on the Coastal Plain of both Virginia and North Carolina found that northern long-eared bat relative activity was highest in areas containing greater proportions of woody wetlands and upland pine-dominated evergreen forests. Conversely, the likelihood to record northern long-eared bats was associated with smaller proportions of woody wetlands and open water resources, emphasizing the importance of upland forests adjacent to these features. I also observed a higher probability of recording northern long-eared bats during non-winter seasons and when temperatures were between 10 and 25 °C, potentially highlighting an optimal thermoneutral zone for the species regionally. Research using presence data from the Monongahela National Forest (MNF) in the Central Appalachians of West Virginia found that northern long-eared bat habitat, whether occupied or not, was abundant (43.1% of the MNF) and widely dispersed. Northern long-eared bat habitat on the MNF was often characterized as mature, interior mixed mesophytic forests. Research using passive acoustic surveys associated with hibernacula in western Virginia found that northern long-eared bats were most active near hibernacula during warmer weeks of the fall swarm and spring emergence, when rainfall was low. Similarly, the probability of northern long-eared bat activity was highest near hibernacula during the spring/summer season. However, unlike relative activity, the likelihood of recording northern long-eared bats was associated with more heterogeneous, interior forests. Finally, research using a combination of long-term repeated and single-season clearance survey data from New England found that northern long-eared bat occupancy was highest on steep hillsides in contiguous forested landscapes with minimal anthropogenic development. My results also indicated higher occupancy of northern long-eared bats in warmer regions, particularly along the New England coastline and offshore islands. These findings collectively stress the importance of managing areas of large core forest to promote sustainable roost formation and productive foraging areas, often associated with dynamic ecotones, to support the survival and recovery of northern long-eared bats in the post-WNS Mid-Atlantic and Northeast. / Doctor of Philosophy / The northern long-eared bat was once one of the most common bat species in North America. However, due to population impacts caused by white-nose syndrome (WNS) the species is now recognized as endangered by the United States Fish and Wildlife Service. In this dissertation, I explore habitat selection and suitability, seasonal activity, and occupancy trends of remnant populations of northern long-eared bats in the Mid-Atlantic and Northeast of the United States, representing approximately 25% of the species' historical range. Specifically, I examined home range size and habitat selection of a reproductively successful maternity colony on the Mid-Atlantic Coastal Plain, overwintering activity at both interior and coastal sites, habitat suitability in the Central Appalachians, and spatial occupancy trends across New England. My research found that reproductive northern long-eared bats actively selected for specific cover features and displayed notable shifts in roost tree selection throughout the maternity season on the Coastal Plain of North Carolina. My research also indicated that northern long-eared bats were more active during non-winter seasons, favoring moderate temperatures and areas of forested wetlands adjacent to evergreen forests in coastal North Carolina and Virginia. In Virginia, northern long-eared bat activity near mountain hibernacula was highest in areas of greater landscape richness prior to and after hibernation. Finally, my research from New England found that northern long-eared bat occupancy was highest in steeper, forested landscapes in the absence of human development. Overall, this research highlights the need to conserve and manage forest ecosystems to promote recovery of the endangered northern long-eared bat. Conservation and management efforts informed by population status, activity trends, and habitat associations will be invaluable in guiding species recovery efforts.

Small Island Developing States (SIDS) of the Caribbean are one of the world’s ‘hottest’ ‘biodiversity hotspots’. However, this biodiversity continues to be threatened by habitat loss, and now, by climate change. The research reported here investigated the potential of species distribution modelling (SDM) as a plant conservation tool within Caribbean SIDS, using Trinidad as a case study. Prior to the application of SDM, ancillary analyses including: (i) quantification and mapping of forest cover change (1969 to 2007) and deforestation rates, and (ii) assessment of the island’s vegetation community distribution and associated drivers were carried out. Community distribution and commercial importance and global/regional rarity were used to generate a list of species for assessing the potential of SDM within Trinidad. Species occurrence data were used to generate species distribution models for present climate conditions within the SDM algorithm, MaxEnt. These results were assessed through expert appraisal and concurrence with results of ecological analyses. These models were used to forecast suitable species climate space forty years into an SRES A2 future. Present and future models were then combined to produce a ‘collective change map’ which showed projected areas of species’ range expansion, contraction or stability for this group of species with respect to Trinidad’s Protected Areas (PAs) network. Despite the models being indicative rather than accurate, it was concluded that species’ climate space is likely to decrease or disappear across Trinidad. Extended beyond Trinidad into the remainder of the Caribbean region, SDM may be a crucial tool in identifying which PAs within the region (and not individual islands) will facilitate future survival of given target species. Consideration of species conservation from a regional, rather than an individual island perspective, is strongly recommended for aiding the Caribbean SIDS to adapt in response to climate change.

Prédire les réponses de la biodiversité aux changements climatiques anthropiques est devenu un champ de recherche avec des enjeux scientifiques et sociétaux majeurs. Mon travail de thèse a consisté à évaluer les impacts du réchauffement climatique sur un parasitoïde de drosophiles, Leptopilina boulardi, à une petite échelle géographique, le sud-est de la France. L'objectif était non seulement d'examiner l'évolution de la distribution du parasitoïde en réponse à une hausse des températures qu'il fallait préciser à cette échelle géographique, mais aussi d'appréhender les adaptations mises en place dans la zone de progression de l'espèce. Dans un premier temps, l'analyse de données d'échantillonnages et de données météorologiques m'ont permis de mettre en évidence une rapide expansion de l'aire de répartition du parasitoïde vers le nord, à un taux moyen de 90km/décennie, simultanément à une augmentation moyenne de la température de 1,57°C ces 30 dernières années, dans l'aire d'étude. Après avoir identifié les principaux facteurs environnementaux, structurant la répartition spatiale de L. boulardi, j'ai modélisé sa distribution potentielle dans le sud-est de la France, sous conditions climatiques actuelles et pour 2050, pour deux scénarios d'émission de CO2. En 2050, la distribution géographique de L. boulardi devrait considérablement s'étendre vers le nord sous l'effet des changements climatiques. Ensuite, en mesurant plusieurs traits d'histoire de vie selon 4 régimes thermiques fluctuants, j'ai montré que les populations de L. boulardi situées en limite d'aire de répartition sont génétiquement différenciées de celles situées dans l'aire centrale de répartition. Le fait que les populations marginales aient une valeur sélective plus importante à faible température suggère une adaptation locale des parasitoïdes dans la zone de progression de l'aire de répartition. La dernière partie de ce travail de thèse a pour objectif de mieux comprendre le processus de colonisation de L. boulardi. Pour cela, j'ai entrepris le développement de marqueurs RAD-sequencing sur 15 populations de cette espèce, distribuées le long d'un cline de latitude dans le sud-est de la France. Les nombreuses données issues du séquençage Illumina me permettront de connaître la structuration génétique de ces populations. L'ensemble de ces résultats obtenus au cours de ma thèse révèlent la force avec laquelle les changements climatiques peuvent impacter les espèces, principalement celles de haut niveau trophique, en provoquant des changements très rapide de distribution et des modifications génotypiques et phénotypiques permettant une meilleure adaptation locale / Predicting biodiversity responses to anthropogenic climate change has become a field of research with major scientific and societal issues. The main goal of my thesis was to evaluate the impacts of global warming on a Drosophila parasitoid, Leptopilina boulardi, at a small geographical scale, the South-East of France. The aim was not only to examine the change in the distribution of the parasitoid in response to rising temperatures, but also to understand the adaptations associated with this change. First, the analysis of insect sampling and meteorological data allowed me to demonstrate a rapid expansion of the parasitoid range to the north with an average rate of 90km/decade as well as a simultaneous temperature increase of 1.57°C on average over the past 30 years in the studied area. Following the identification of the main environmental factors structuring the spatial distribution of L. boulardi, I fitted a model predicting its potential distribution in the south-east of France, under the current climate and in 2050, for two CO2 emission scenarios. In 2050, the geographical distribution of L. boulardi should significantly extend northward as a result of climate change. Then, by measuring several life history traits under four fluctuating temperature regimes, I have shown that populations of L. boulardi located on the border of the range are genetically differentiated from those in the central range. The fact that marginal populations have a greater fitness at low temperature suggests local adaptation of parasitoids in the area of progression of range. The last part of this thesis aimed to better understand the process of colonization of L. boulardi. For this, I undertook the development of RAD-sequencing markers to genotype 15 populations of this species distributed along a cline of latitude in the southeast of France. Numerous data from Illumina sequencing will allow me to characterize the genetic structure of the populations. All the results obtained in my thesis highlight the force with which climate change may impact species, in particular those of high trophic level, causing rapid changes in distribution along with genotypic and phenotypic changes underlying local adaptation

<p>U&nbsp; radu&nbsp; je&nbsp; analizirana&nbsp; efektivnost&nbsp; za&scaron;tićenih područja&nbsp; Srbije&nbsp; u&nbsp; sada&scaron;njosti&nbsp; i&nbsp; budućnosti&nbsp; na osnovu&nbsp; zastupljenosti&nbsp; povoljnih&nbsp; stani&scaron;ta&nbsp; i centara&nbsp; diverziteta&nbsp; 116&nbsp; običnih&nbsp; vrsta&nbsp; ptica odabranih na osnovu 11 kriterijuma. Zasebno su evaluirana&nbsp; za&scaron;tićena&nbsp; prirodna&nbsp; dobara, međunarodno značajna područja za ptice (IBA) i mreža nastala preklapanjem dva tipa za&scaron;tićenih područja.&nbsp; Povoljna&nbsp; stani&scaron;ta&nbsp; istraživanih&nbsp; vrsta utvrđena su modelovanjem distribucije vrsta uz pomoć&nbsp; MaxEnt&nbsp; pristupa,&nbsp; a&nbsp; modeli&nbsp; distribucije projektovani&nbsp; su&nbsp; na&nbsp; četiri&nbsp; različita&nbsp; scenarija klimatskih&nbsp; promena&nbsp; u&nbsp; budućnosti&nbsp; (2050. godina).&nbsp; IBA&nbsp; mreža&nbsp; pokazala&nbsp; se&nbsp; kao&nbsp; značajno<br />efektivnija za za&scaron;titu stani&scaron;ta istraživanih vrsta i centara&nbsp; njihvog&nbsp; diverziteta&nbsp; u&nbsp; odnosu&nbsp; na&nbsp; mrežu za&scaron;tićenih&nbsp; prirodnih&nbsp; dobara,&nbsp; a&nbsp; slična&nbsp; situacija predviđena&nbsp; je&nbsp; i&nbsp; u&nbsp; budućnosti.&nbsp; Oba&nbsp; tipa za&scaron;tićenih&nbsp; područja&nbsp; pokrivala&nbsp; su&nbsp; u&nbsp; proseku srazmerno&nbsp; mali&nbsp; procenat&nbsp; povoljnih&nbsp; stani&scaron;ta istraživanih&nbsp; vrsta&nbsp; (za&scaron;tićena&nbsp; prirodna&nbsp; dobra&nbsp; &ndash;<br />10,4%;&nbsp; IBA&nbsp; &ndash;&nbsp; 21,9%)&nbsp; i&nbsp; dovela&nbsp; su&nbsp; do ostvarivanja konzervacionih ciljeva malog broja vrsta (za&scaron;tićena prirodna dobra&nbsp; &ndash;&nbsp; 11; IBA&nbsp; -&nbsp; 37), dok&nbsp; su&nbsp; centri&nbsp; diverziteta&nbsp; istraživanih&nbsp; vrstasrazmerno&nbsp; slabo&nbsp; zastupljeni&nbsp; unutar&nbsp; obe&nbsp; mreže (za&scaron;tićena&nbsp; prirodna&nbsp; dobra&nbsp; &ndash;&nbsp; 9,8%;&nbsp; IBA&nbsp; &ndash; 25,4%).&nbsp; Za&scaron;tićena&nbsp; područja&nbsp; nisu&nbsp; pokazale<br />značajno&nbsp; veću&nbsp; efektivnost&nbsp; za&nbsp; konzervaciono prioritetnt&nbsp; vrste&nbsp; i&nbsp; njihov&nbsp; diverzitet.&nbsp; Za&scaron;tićena prirodna&nbsp; dobra&nbsp; i&nbsp; IBA&nbsp; mreža&nbsp; u&nbsp; Srbiji&nbsp; značajno bolje&nbsp; pokrivaju&nbsp; stani&scaron;ta&nbsp; i&nbsp; centre&nbsp; diverziteta &scaron;umskih vrsta i vrsta kamenjara, klisura i litica, dok&nbsp; su&nbsp; povoljna&nbsp; stani&scaron;ta&nbsp; i&nbsp; centri&nbsp; diverziteta gnezdarica&nbsp; poljoprivrednih&nbsp; stani&scaron;ta,&nbsp; naselja&nbsp; i vodenih&nbsp; stani&scaron;ta&nbsp; izrazito&nbsp; slabo&nbsp; zastupljena. Stani&scaron;ta&nbsp; gnezdarica&nbsp; nizijskih&nbsp; poljoprivrednih<br />stani&scaron;ta&nbsp; naročito&nbsp; su&nbsp; slabo&nbsp; zastupljena&nbsp; unutar za&scaron;tićenih&nbsp; prirodnih&nbsp; dobara&nbsp; i&nbsp; IBA&nbsp; mreže,&nbsp; koja za&nbsp; ovu&nbsp; grupu&nbsp; nisu&nbsp; dovela&nbsp; do&nbsp; postizanja konzervacionih&nbsp; ciljeva.&nbsp; Razlike&nbsp; u&nbsp; efektivnosti za&scaron;tićenih&nbsp; područja&nbsp; za&nbsp; gnezdarice&nbsp; različitih tipova&nbsp; stani&scaron;ta&nbsp; u&nbsp; budućnosti&nbsp; će&nbsp; se&nbsp; generalno povećavati,&nbsp; usled&nbsp; predviđenog&nbsp; smanjivanja<br />areala većine &scaron;umskih vrsta koje će se povlačiti u&nbsp; za&scaron;titom&nbsp; bolje&nbsp; pokrivene&nbsp; planinske&nbsp; predele&nbsp; i &scaron;irenja areala većine gnezdarica poljoprivrednih i&nbsp; vodenih&nbsp; stani&scaron;ta&nbsp; na&nbsp; neza&scaron;tićena&nbsp; nizijska područja. Za deo vrsta među kojima dominiraju<br />gnezdarice&nbsp; brdsko-planinskih&nbsp; &scaron;umskih&nbsp; i&nbsp; drugih prirodnih&nbsp; stani&scaron;ta&nbsp; glavna&nbsp; strategija&nbsp; za&scaron;tite podrazumeva&nbsp; precizno&nbsp; pro&scaron;irenje&nbsp; granica sada&scaron;njih&nbsp; za&scaron;tićenih&nbsp; područja&nbsp; uz&nbsp; upravljanje orentisano&nbsp; ka&nbsp; očuvanju&nbsp; prirodnih&nbsp; stani&scaron;ta&nbsp; i smanjenju&nbsp; iskori&scaron;ćavanja&nbsp; resursa.&nbsp; Sa&nbsp; druge strane,&nbsp; za&nbsp; većinu&nbsp; gnezdarica&nbsp; poljoprivrednih&nbsp; i<br />travnih stani&scaron;ta, naročito u nizijskim predelima, efektivna&nbsp; strategija&nbsp; bila&nbsp; bi&nbsp;&nbsp; definisanje&nbsp; potpuno novih&nbsp; i&nbsp; prostranih&nbsp; za&scaron;tićenih&nbsp; područja orijentisanih&nbsp; ka&nbsp; održavanju&nbsp; povoljnog&nbsp; režima upravljanja&nbsp; i&nbsp; kori&scaron;ćenja&nbsp; prostora.&nbsp; Rad&nbsp; ukazuje<br />na velike mogućnosti kori&scaron;ćenja nesistematično prikupljenih&nbsp; podataka&nbsp; profesionalnih&nbsp; i amaterskih&nbsp; ornitologa&nbsp; uz&nbsp; primenu&nbsp; tehnika modelovanja&nbsp; distribucije&nbsp; vrsta,&nbsp; ali&nbsp; nagla&scaron;ava potrebu&nbsp; za&nbsp; pokretanjem&nbsp; &scaron;irokih&nbsp; programa<br />sistematskog&nbsp; popisa,&nbsp; kartiranja&nbsp; i&nbsp; monitoringa običnih vrsta ptica.</p> / <p>The&nbsp; study&nbsp;&nbsp; analyzes&nbsp; the&nbsp; effectiveness&nbsp; of protected areas in Serbia presently as well as in the&nbsp; future,&nbsp; based&nbsp; on&nbsp; the&nbsp; representation&nbsp; of suitable habitats and centers of diversity for 116 common&nbsp; species of&nbsp; birds,&nbsp; selected on the&nbsp; basis of&nbsp; 11&nbsp; criteria.&nbsp; Nationally&nbsp; protected&nbsp; areas, Important&nbsp; Bird&nbsp; and&nbsp; Biodiversity&nbsp; areas&nbsp; (IBAs) and&nbsp; networks formed&nbsp; by overlapping these two types&nbsp; of&nbsp; protected&nbsp; areas&nbsp; have&nbsp; been&nbsp; evaluated separately. Suitable habitats of the species in the study&nbsp; were&nbsp; determined&nbsp; by&nbsp; species&nbsp; distribution modeling&nbsp; using&nbsp; the&nbsp; MaxEnt&nbsp; approach,&nbsp; and&nbsp; the distribution&nbsp; models&nbsp; were&nbsp; projected&nbsp; to&nbsp; four different&nbsp; climate&nbsp; change&nbsp; scenarios&nbsp; in&nbsp; future (year&nbsp; 2050).&nbsp; The&nbsp; IBA&nbsp; network&nbsp; proved&nbsp; to&nbsp; be significantly more effective for the&nbsp; protection of habitats&nbsp; of&nbsp; studied&nbsp; species&nbsp; and&nbsp; centers&nbsp; of&nbsp; their diversity, compared&nbsp; to the network of nationally protected&nbsp; areas,&nbsp; and&nbsp; a&nbsp; similar&nbsp; situation&nbsp; is projected for the future. Both types of protected areas&nbsp; on&nbsp; average&nbsp; covered&nbsp; a&nbsp; relatively&nbsp; small percentage of suitable habitats for most species (10.4%&nbsp; in&nbsp; nationaly&nbsp; protected&nbsp; areas,&nbsp; 21.9%&nbsp; in IBA)&nbsp; and&nbsp; meet&nbsp; conservation&nbsp; goals&nbsp; only&nbsp; for&nbsp; a&nbsp; small&nbsp; number&nbsp; of&nbsp; species&nbsp; (11&nbsp; for&nbsp; nationaly protected&nbsp; areas,&nbsp; 37&nbsp; for&nbsp; IBA).&nbsp; Diversity&nbsp; centers for&nbsp; species&nbsp; in&nbsp; the&nbsp; study&nbsp; are&nbsp; relatively&nbsp; poorlyrepresented within all three networks&nbsp; (9.8% for nationaly&nbsp; protected&nbsp; areas&nbsp; and&nbsp; 25.4%&nbsp; for&nbsp; IBA). Protected&nbsp; areas&nbsp; did&nbsp; not&nbsp; show&nbsp; significantly higher&nbsp; effectiveness&nbsp; for&nbsp; the&nbsp; conservation&nbsp; of priority&nbsp; species&nbsp; and&nbsp; their&nbsp; diversity.&nbsp; Nationaly protected&nbsp; areas&nbsp; and&nbsp; the&nbsp; IBA&nbsp; network&nbsp; in&nbsp; Serbia have&nbsp; a&nbsp; significantly&nbsp; better&nbsp; coverage&nbsp; of&nbsp; habitats and&nbsp; centers&nbsp; of&nbsp; diversity&nbsp; for&nbsp; forest&nbsp; species&nbsp; and species&nbsp; of&nbsp; rocky&nbsp; habitats,&nbsp; cliffs&nbsp; and&nbsp; gorges, while&nbsp; suitable&nbsp; habitats&nbsp; and&nbsp; centers&nbsp; of&nbsp; diversity for breeding birds of farmlands, settlements and aquatic&nbsp; habitats&nbsp; are&nbsp; very&nbsp; poorly&nbsp; represented. Habitats of breeding birds of lowland&nbsp; armlands are&nbsp; particularly&nbsp; poorly&nbsp; represented&nbsp; within protected&nbsp; natural&nbsp; assets&nbsp; and&nbsp; the&nbsp; IBA&nbsp; network, and this measure does not meet the conservation goals for this group of birds. Differences in the effectiveness&nbsp; of&nbsp; protected&nbsp; areas&nbsp; for&nbsp; breeding birds&nbsp; of&nbsp; various&nbsp; habitat&nbsp; types&nbsp; will&nbsp; generally increase&nbsp; in&nbsp; the&nbsp; future,&nbsp; due&nbsp; to&nbsp; the&nbsp; anticipated range decrease&nbsp; for&nbsp; most forest species that will withdraw&nbsp; to&nbsp; the&nbsp; better&nbsp; conserved&nbsp; mountainous areas, whereas range of the majority o f breeding birds&nbsp; of&nbsp; farmland&nbsp; and&nbsp; aquatic&nbsp; habitats&nbsp; will&nbsp; be expanded&nbsp; to&nbsp; unprotected&nbsp; lowland&nbsp; areas.&nbsp; For some&nbsp; of&nbsp; the&nbsp; species,&nbsp; mostly&nbsp; birds&nbsp; of&nbsp; hill&nbsp; and mountain&nbsp; forests and other natural&nbsp; habitats, the main&nbsp; conservation&nbsp; strategy&nbsp; implies&nbsp; precise boundaries&nbsp; extension&nbsp; of&nbsp; the&nbsp; current&nbsp; protected areas&nbsp; with&nbsp; management&nbsp; directed&nbsp; towards preserving&nbsp; natural&nbsp; habitats&nbsp; and&nbsp; reducing&nbsp; the utilization&nbsp; of&nbsp; resources.&nbsp; On&nbsp; the&nbsp; other&nbsp; hand,&nbsp; for most&nbsp; of&nbsp; the&nbsp; farmland&nbsp; and&nbsp; grassland&nbsp; species, especially in the lowlands, an effective strategy would&nbsp; be&nbsp; to&nbsp; define&nbsp; completely&nbsp; new&nbsp; and spacious&nbsp; protected&nbsp; areas&nbsp; oriented&nbsp; towards maintaining a favorable regime for management and&nbsp; landuse. The&nbsp; study&nbsp; demonstrates that there are&nbsp; great&nbsp; possibilities&nbsp; of&nbsp; using&nbsp; nonsystematically&nbsp; collected&nbsp; data&nbsp; from&nbsp; professiona l and&nbsp; amateur&nbsp; ornithologists,&nbsp; for&nbsp; application&nbsp; in species&nbsp; distribution&nbsp; modeling,&nbsp; but&nbsp; also emphasizes&nbsp; the&nbsp; need&nbsp; to&nbsp; launch&nbsp; extensive programs for systematic inventory, mapping and monitoring of common bird species.</p>

Interannual variability of Humboldt squid (Dosidicus gigas) occurrence in the northern California Current System is largely unknown. In Oregon, the distribution of this versatile predator and what is influencing their range expansion from Mexico is poorly understood due to the recent nature of their "invasion" and a lack of monitoring. Humboldt squid are large predators that have the potential to affect ecosystem structure and fisheries because of their high-energy demands and ability to exploit a variety of oceanographic conditions and prey sources. Developing baseline distribution information is a critical first step to assess their potential ecological, social, and economic impacts, and to develop models to predict future range expansion. This study has two main objectives: (1) to document where and when Humboldt squid have been present in Oregon through cooperative fisheries research, and (2) to correlate the sightings with oceanographic conditions using a geographic information system (GIS) and species distribution modeling (SDM). I conducted 54 interviews with local fishermen and aggregated their squid sightings with available fishery-independent survey and fishery-dependent observer data from the National Marine Fisheries Service. I compiled a total of 339 Humboldt squid sightings, reported for the years 2002-2011 from the Oregon coast to 131�� west longitude. Correlation analyses were performed for Humboldt squid sightings and sea surface temperature (SST), chlorophyll a content (chla), sea surface height anomalies (SSH), dissolved oxygen at 30 m depth (30 m DO), and sea surface salinity (SSS) using a GIS, nonparametric multiplicative regression (NPMR) habitat modeling, and maximum entropy modeling (Maxent). Results indicate that oceanographic conditions have the potential to influence Humboldt squid occurrence, and in Oregon, sightings vary temporally and spatially. Combining the sightings from fishermen and scientific surveys greatly enhanced the spatial extent of the data. Humboldt squid were most frequently observed between 124.4��W and 125��W in proximity to the shelf-break at the 200 m isobath, with peak sightings (116) recorded in 2009 and the fewest (6) reported in 2003 and 2011. The highest occurrence of Humboldt squid were observed at a SST of 10.5-13.0��C, 0.26-3.0 mg m����� chla content, -4.0-1.0 m SSH anomalies, 32.2-32.8 psu SSS, and at 3-4.5 ml L����� and 6-7 ml L����� 30 m depth DO. Maps of estimated likelihood of occurrence generated by NPMR were consistent with overlayed observations from fishermen, which were not used in the model because they were limited to presence-only information. An interdisciplinary approach that incorporates cooperative fisheries research and ecosystem-based management is necessary for monitoring Humboldt squid in Oregon. Traditional methods are insufficient because Humboldt squid are data-poor, highly migratory, and are main predators of many commercially important fisheries in Oregon. Based on my findings, sightings recorded by fishermen covered a much larger area over a longer time frame than the scientific survey and observer data, and excluding their knowledge would have led to a different interpretation of Humboldt squid distribution and environmental tolerances. Although there is uncertainty in the data from potential map bias or misidentification of smaller Humboldt squid, incorporating sightings from fishermen with traditional fisheries research increases the quantity and quality of information. Cooperative monitoring for Humboldt squid could include training in species identification and sea condition reporting in logbooks. Future "invasions" are likely, and more eyes on the water will improve our understanding of the behavior and impacts of Humboldt squid on coastal resources. / Graduation date: 2013

The work describes the processing and analysis of remote sensing time series data for a comparative assessment of changes in different tropical rainforest areas in East Africa. In order to assess the effects of the derived changes in land cover and forest fragmentation, the study made use of spatially explicit modelling approaches within a geographical information system (GIS) to extrapolate sets of biological field findings in space and time. The analysis and modelling results were visualised aiming to consider the requirements of three different user groups. In order to evaluate measures of forest conservation and to derive recommendations for an effective forest management, quantitative landscape-scale assessments of land cover changes and their influence on forest biodiversity patterns are needed. However, few remote sensing studies have accounted for all of the following aspects at the same time: (i) a dense temporal sequence of land cover change/forest fragmentation information, (ii) the coverage of several decades, (iii) the distinction between multiple forest formations and (iv) direct comparisons of different case studies. In regards to linkages of remote sensing with biological field data, no attempts are known that use time series data for quantitative statements of long-term landscape-scale biodiversity changes. The work studies three officially protected forest areas in Eastern Africa: the Kakamega-Nandi forests in western Kenya (focus area) and Mabira Forest in south-eastern Uganda as well as Budongo Forest in western Uganda (for comparison purposes). Landsat imagery of in total eight or seven dates in regular intervals from 1972/73 to 2003 was used. Making use of supervised multispectral image classification procedures, in total, 12 land cover classes (six forest formations) were distinguished for the Kakamega-Nandi forests and for Budongo Forest while for Mabira Forest ten classes could be realised. An accuracy assessment via error matrices revealed overall classification accuracies between 81% and 85%. The Kakamega-Nandi forests show a continuous decrease between 1972/73 and 2001 of 31%, Mabira Forest experienced an abrupt loss of 24% in the late 1970s/early 1980s, while Budongo Forest shows a relatively stable forest cover extent. An assessment of the spatial patterns of forest losses revealed congruence with areas of high population density while a spatially explicit forest fragmentation index indicates a strong correlation of forest fragmentation with forest management regime and forest accessibility by roads. For the Kenyan focus area, three sets of biological field abundance data on keystone species/groups were used for a quantitative assessment of the influence of long-term changes in tropical forests on landscape-scale biodiversity patterns. For this purpose, the time series was extended with another three land cover data sets derived from aerial photography (1965/67, 1948/(52)) and old topographic maps (1912/13). To predict the spatio-temporal distribution of the army ant Dorylus wilverthi and of ant-following birds, GIS operators (i.e. focal and local functions) and statistical tests (i.e. OLS or SAR regression models) were combined into a spatial modelling procedure. Abundance data on three guilds of birds differing in forest dependency were directly extrapolated to five forest cover classes as distinguished in the time series. The results predict declines in species abundances of 56% for D. wilverthi, of 58% for ant-following birds and an overall loss of 47% for the bird habitat guilds, which in all three cases greatly exceed the rate of forest loss (31%). Additional extrapolations on scenarios of deforestation and reforestation confirmed the negative ecological consequences of splitting-up contiguous forest areas but also showed the potential of mixed indigenous forest plantings. The visualisation of the analysis and modelling results produced a mixture of different outcomes. Map series and a matrix of maps both showing species distributions aim to address scientists and decision makers. The results of the land cover change analysis were synthesised in a map of land cover development types for each study area, respectively. These maps are designed mainly for scientists. Additional maps of change, limited to a single class of forest cover and to three dates were generated to ensure an easy-to-grasp communication of the major forest changes to decision makers. Additionally, an easy-to-handle visualisation tool to be used by scientists, decision makers and local people was developed. For the future, an extension of this study towards a more complete assessment including more species/groups and also ecosystem functions and services would be desirable. Combining a framework for land cover simulation with a framework for running empirical extrapolation models in an automated manner could ideally result in a GIS-based, integrated forest ecosystem assessment tool to be used as regional spatial decision support system. / Die Arbeit beschreibt die Prozessierung und Analyse von Fernerkundungs-Zeitreihendaten für eine vergleichende Abschätzung von Veränderungen verschiedener tropischer Waldökosysteme Ostafrikas. Um Effekte der Veränderungen bzgl. Landbedeckung und Waldfragmentierung auf Biodiversitätsmuster abzuschätzen, wurden verschiedene räumlich explizite Modellierungssätze innerhalb eines geographischen Informationssystems (GIS) zur räumlichen und zeitlichen Extrapolation biologischer Felderhebungsdaten benutzt. Die Visualisierung der Analyse- und Modellierungsergebnisse erfolgte unter Berücksichtigung der Bedürfnisse von drei verschiedenen Nutzergruppen. Um Waldschutzmaßnahmen zu evaluieren und Empfehlungen für ein effektives Waldmanagement abzuleiten, sind quantitative Abschätzungen von Landbedeckungsveränderungen sowie von deren Einfluss auf tropische Waldbiodiversitätsmuster nötig. Wenige fernerkundungsbasierte Studien haben jedoch bislang alle der folgenden Faktoren berücksichtigt: (i) Informationen zu Veränderungen von Landbedeckung und Waldfragmentierung in dichter zeitlicher Sequenz, (ii) die Abdeckung mehrerer Jahrzehnte, (iii) die Unterscheidung zwischen mehreren Waldformationen, und (iv) direkte Vergleiche von unterschiedlichen Fallstudien. Hinsichtlich Verknüpfungen von Fernerkundung mit biologischen Felddaten sind bisher keine Studien bekannt, die Zeitreihendaten für quantitative Aussagen zu Langzeitveränderungen von Biodiversität auf Landschaftsebene verwenden. Die Arbeit untersucht drei offiziell geschützte Gebiete: die Kakamega-Nandi forests in Westkenia (Hauptuntersuchungsgebiet) sowie Mabira Forest in Südost-Uganda und Budongo Forest in West-Uganda (zu Vergleichszwecken). Es wurden Landsat-Daten für insgesamt acht bzw. sieben Zeitpunkte zwischen 1972/73 und 2003 in ungefähr gleichen Abständen erworben. Mit Hilfe von überwachten, multispektralen Klassifizierungsverfahren wurden für die Kakamega-Nandi forests und Budongo Forest jeweils 12 Landbedeckungsklassen (sechs Waldformationen) und für Mabira Forest zehn Klassen unterschieden. Eine Genauigkeitsprüfung mit Hilfe von Fehlermatrizen ergab Gesamtklassifizierungsgenauigkeiten zwischen 81% und 85%. Die Kakamega-Nandi forests sind durch eine kontinuierliche Waldabnahme von 31% zwischen 1972/73 und 2001 gekennzeichnet, Mabira Forest zeigt einen abrupten Waldverlust von 24% in den späten 1970ern/frühen 1980ern, während die Ergebnisse für Budongo Forest eine relativ stabile Waldbedeckung ausweisen. Während eine Abschätzung der räumlichen Muster von Waldverlusten eine hohe Deckungsgleichheit mit Gebieten hoher Bevölkerungsdichte ergab, deutet die Anwendung eines räumlich expliziten Waldfragmentierungsindexes auf eine starke Korrelation von Waldfragmentierung mit der Art von Waldmanagement sowie mit der Erreichbarkeit von Wald über Straßen hin. Um den Einfluss von Langzeit-Landbedeckungsveränderungen auf Biodiversitätsmuster auf Landschaftsebene für das kenianische Hauptuntersuchungsgebiet quantitativ abzuschätzen wurden drei Datensätze mit biologischen Felderhebungen zur Abundanz von Schlüsselarten/-gruppen verwendet. Zu diesem Zweck wurde die Zeitreihe zunächst um drei weitere Landbedeckungs-Datensätze ergänzt, die aus Luftbildern (1965/67, 1948/(52)) bzw. alten topographischen Karten (1912/13) gewonnen wurden. Zur Vorhersage der raum-zeitlichen Verteilung der Treiberameise Dorylus wilverthi wurden GIS-Operatoren und statistische Tests (OLS bzw. SAR Regressionsmodelle) in einem räumlichen Modellierungsablauf kombiniert. Abundanzdaten von drei sich hinsichtlich ihrer Abhängigkeit von Wald unterscheidenden Vogelgilden wurden direkt auf fünf Waldbedeckungsklassen hochgerechnet, die in der Zeitreihe unterschieden werden konnten. Die Ergebnisse prognostizieren Abundanzabnahmen von 56% für D. wilverthi, von 58% für Ameisen-folgende Vögel und einen Gesamtverlust von 47% für die Vogelgilden, was in allen drei Fällen eine deutliche Überschreitung der Waldverlustrate von 31% darstellt. Zusätzliche Extrapolationen basierend auf Szenarien bestätigten die negativen ökologischen Konsequenzen der Zerteilung zusammenhängender Waldflächen bzw. zeigten andererseits das Potential von Aufforstungen mit einheimischen Arten auf. Die Visualisierung der Analyse- bzw. Modellierungsergebnisse führte zu unterschiedlichen Darstellungen: mit einer Reihe von nebeneinander positionierten Einzelkarten sowie einer Matrix von Einzelkarten, die jeweils Artenverteilungen zeigen, sollen Wissenschaftler und Entscheidungsträger angesprochen werden. Aus den Ergebnissen der Landbedeckungsanalyse für die drei Untersuchungsgebiete wurden Landbedeckungsveränderungstypen generiert und jeweils in einer synthetischen Karte dargestellt, die hauptsächlich für Wissenschaftler gedacht sind. Um die wesentlichen Waldveränderungen auch auf einfache Weise zu den Entscheidungsträgern zu kommunizieren, wurden zusätzliche Karten erstellt, die nur eine aggregierte Klasse „Waldbedeckung“ zeigen und jeweils auf drei Zeitschritte der Zeitreihen begrenzt sind. Zusätzlich wurde ein leicht zu bedienendes Visualisierungstool entwickelt, das für Wissenschaftler, Entscheidungsträger und die lokale Bevölkerung gedacht ist. Für die Zukunft wäre eine umfassendere Abschätzung unter Berücksichtigung zusätzlicher Arten/-gruppen sowie auch Ökosystemfunktionen und –dienstleistungen wünschenswert. Die Verknüpfung einer Applikation zur Landbedeckungsmodellierung mit einer Applikation zur Ausführung von empirischen Extrapolationsmodellen (in stärkerem Maße automatisiert als in dieser Arbeit) könnte im Idealfall in ein GIS-basiertes Tool zur integrativen Bewertung von Waldökosystemen münden, das dann als räumliches Entscheidungsunterstützungssystem verwendet werden könnte.

Over the last 3 decades, freshwater aquaculture has become one of the most important food industries. However the constant introduction of a reduced number of very successful species for aquaculture has been identified as one of the main activities related to the alarming decline of fish biodiversity worldwide. This issue has raised awareness amongst the scientific community, governmental authorities and the general public towards freshwater fish biodiversity. This new awareness has promoted the development of “green” markets and environmentally friendly strategies, aiming for a reliable production of protein sources. The development of native species aquaculture has been presented as a strong alternative for sustainable aquaculture and the protection of biodiversity. However, it seems clear that unplanned native species aquaculture developments can be as detrimental on local biodiversity as the introduction of exotic fish, if not more dangerous. Therefore, the advantages and disadvantages of native species aquaculture have to be clearly analysed before any aquaculture development. This study aimed to establish a philosophical background regarding the use of native fish species in aquaculture in contrast to the introduction of exotic species that may compete for a similar niche as food in local markets. The main ecological impacts that exotic fish species may have on natives, such as competition, predation, and hybridization were discussed. In addition, a well planned native species Aquaculture Strategy for the Protection of Biodiversity was produced, at catchment level, within a Geographic Information System (GIS). For the development of the native species aquaculture strategy in central Mexico, four species of Atherinids (Chirostoma estor, C. Jordani, C. promelas and Atherinella balsana) and two species of native Ictalurids (Ictalurus balsanus and Ictalurus dugesii) were included in this study. These six species are relatively new to aquaculture and they were selected on the basis of their importance in local fisheries and markets in their native basins of the Lerma-Santiago and Balsas rivers. Both of these basins are of great importance in central Mexico, not only because of their biodiversity but also because of their high human population densities and socio-economic status. The use of Geographic Information Systems was a fundamental factor in the development of the native species aquaculture strategy at catchment level, consisting of site suitability models (SSM) for each species in their corresponding native catchments. Overall, SSM identified 13,916 km2 and 11,178 km2 highly suitable for aquaculture of the studied Atherinids and Ictalurids respectively, based on Water, Soil and Terrain, Infrastructure and Risk sub-models. A set of predictive species distribution models (PSDM), which related ecological characteristics for each studied species with relevant environmental and topographic parameters into a GIS, were also produced. Such models were developed for the establishment of potential natural ranges of distribution for each species, as well as their potential to become exotic in new environments, as a potential for invasion model (PI). Based on a partial verification, both PSDM and PI models produced results that were satisfactorily consistent with the known distribution of each modelled species. The combination of SSM and PSDM produced an Aquaculture Strategy for the Protection of Biodiversity model (ASPB) which identified the most environmentally friendly suitable areas for aquaculture sites. In contrast, the combination of the SSM with PI models into an ASPB model identified the site suitability potential for non-native species that are genetically close to native ones, in an attempt to reduce the known impacts that exotic species have on local biodiversity. In this way the ASPB model identified 7,651 km2 suitable for aquaculture of I. balsanus in its native Balsas basin and 15,633 km¬2 suitable for aquaculture of the non-native I. dugesii. ASPB models were produced for all the studied species. The final results were used to produce a set of guidelines for the development of sustainable aquaculture of native species at catchment level that cover genetic and ecological implications, as well as a well planned decision making tool produced in a GIS.

When we develop and use species distribution models to predict species' current or potential distributions, we are faced with the trade-offs between model generality, precision, and realism. It is important to know how to improve and validate model generality while maintaining good model precision and realism. However, it is difficult for ecologists to evaluate species distribution models using field-sampled data alone because the true species response function to environmental or ecological factors is unknown. Species distribution models should be able to approximate the true characteristics and distributions of species if ecologists want to use them as reliable tools. Simulated data provide the advantage of being able to know the true species-environment relationships and control the causal factors of interest to obtain insights into the effects of these factors on model performance. I used a case study on Bythotrephes longimanus distributions from several hundred Ontario lakes and a simulation study to explore the effects on model performance caused by several factors: the choice of predictor variables, the model evaluation methods, the quantity and quality of the data used for developing models, and the strengths and weaknesses of different species distribution models. Linear discriminant analysis, multiple logistic regression, random forests, and artificial neural networks were compared in both studies. Results based on field data sampled from lakes indicated that the predictive performance of the four models was more variable when developed on abiotic (physical and chemical) conditions alone, whereas the generality of these models improved when including biotic (relevant species) information. When using simulated data, although the overall performance of random forests and artificial neural networks was better than linear discriminant analysis and multiple logistic regression, linear discriminant analysis and multiple logistic regression had relatively good and stable model sensitivity at different sample size and detection limit levels, which may be useful for predicting species presences when data are limited. Random forests performed consistently well at different sample size levels, but was more sensitive to high detection limit. The performance of artificial neural networks was affected by both sample size and detection limit, and it was more sensitive to small sample size.

When we develop and use species distribution models to predict species' current or potential distributions, we are faced with the trade-offs between model generality, precision, and realism. It is important to know how to improve and validate model generality while maintaining good model precision and realism. However, it is difficult for ecologists to evaluate species distribution models using field-sampled data alone because the true species response function to environmental or ecological factors is unknown. Species distribution models should be able to approximate the true characteristics and distributions of species if ecologists want to use them as reliable tools. Simulated data provide the advantage of being able to know the true species-environment relationships and control the causal factors of interest to obtain insights into the effects of these factors on model performance. I used a case study on Bythotrephes longimanus distributions from several hundred Ontario lakes and a simulation study to explore the effects on model performance caused by several factors: the choice of predictor variables, the model evaluation methods, the quantity and quality of the data used for developing models, and the strengths and weaknesses of different species distribution models. Linear discriminant analysis, multiple logistic regression, random forests, and artificial neural networks were compared in both studies. Results based on field data sampled from lakes indicated that the predictive performance of the four models was more variable when developed on abiotic (physical and chemical) conditions alone, whereas the generality of these models improved when including biotic (relevant species) information. When using simulated data, although the overall performance of random forests and artificial neural networks was better than linear discriminant analysis and multiple logistic regression, linear discriminant analysis and multiple logistic regression had relatively good and stable model sensitivity at different sample size and detection limit levels, which may be useful for predicting species presences when data are limited. Random forests performed consistently well at different sample size levels, but was more sensitive to high detection limit. The performance of artificial neural networks was affected by both sample size and detection limit, and it was more sensitive to small sample size.

Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2016-05-19T19:46:17Z No. of bitstreams: 2 Dissertação - André Felipe Alves de Andrade - 2016.pdf: 2007118 bytes, checksum: 69341ce5bc6c459857d1feff5d92366e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-05-20T13:54:17Z (GMT) No. of bitstreams: 2 Dissertação - André Felipe Alves de Andrade - 2016.pdf: 2007118 bytes, checksum: 69341ce5bc6c459857d1feff5d92366e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2016-05-20T13:54:17Z (GMT). No. of bitstreams: 2 Dissertação - André Felipe Alves de Andrade - 2016.pdf: 2007118 bytes, checksum: 69341ce5bc6c459857d1feff5d92366e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2016-02-26 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Coral reefs are of extreme importance to both nature and society, due to being responsible for several services and harbouring hundreds of species. Despite such critical importance, reef corals current suffered heavy losses since the Anthropocene, with 20% of world´s corals damaged beyond recovery due to human pressure and coastal development. This scenario is even worse, since corals are especially vulnerable to climate change and the entire ecosystem could go extinct by 2050. In this study we focus on comparing the already established impacts from human development and the yet happen losses from climate change on Brazilian corals, a unique fauna that still have gaps in knowledge. We created environmental suitability models for 24 species and quantified individual losses from both climate change and human activities. From the individual results we derived an overall pattern, in which we found out that future losses from climate alteration are equivalent to current losses from human activities. We then used the spatial distribution of those activities and key areas for conservation, determined with software Zonation, to select six areas in the Brazilian exclusive economic zone where proactive and reactive conservation strategies should be implanted, given its importance to biodiversity and concentrated anthropogenic impacts. Overall suitability losses were of approximately 30% for both sources and 60% of the areas will continue to be suitable in the future. Therefore, Brazilian corals will experience heavy losses from climate, especially the loss of highly suitable areas, which are compared to effects from human economic activities. Coral situation is likely to be even worse, if we were to consider bleaching, ocean acidification and diseases, events expected to increase with the rising temperature. / Ecological Niche Modelling (ENM) is widely used for conservation purposes, predicting species invasion, evolutionary aspects and a whole array of applications. However, for most cases, evaluating the efficiency of those models poses as problematic, as commonly used methods (i.e. random methods) do not assure the required independence between data used to create the model and data used to evaluate the model. We developed a new transferabilitybased framework that ensures the much-needed independence between subsets. We created an alternate approach that geographically splits occurrence datasets, while intrinsically controls issues related to previous transferability approaches, such as overfitting, extrapolation and sampling bias. We used 26 Atlantic coral species to perform three different geographical divisions quantifying the effect of different splits on model predictive efficiency. We demonstrate that transferability should be used as an effective method to evaluate ENMs. Geographical split of the area in deciles proved as a reliable evaluation method, assuring independence between datasets and being less prone to common transferability issues. Our odds-and-evens framework provides improvements to the ongoing debate of ENMs evaluating by its transferability. This new method corrects the issue of artificiality causing sampling bias and overfitting, common in previous methodologies, while also is less prone to extrapolation issues, a common problem in transferability approaches. Moreover, the framework appears as a feasible and useful alternative to the problematic and commonly used random partition of datasets evaluation.