6,393 research outputs found
Censored Data Regression in High-Dimension and Low-Sample Size Settings For Genomic Applications
New high-throughput technologies are generating various types of high-dimensional genomic and proteomic data and meta-data (e.g., networks and pathways) in order to obtain a systems-level understanding of various complex diseases such as human cancers and cardiovascular diseases. As the amount and complexity of the data increase and as the questions being addressed become more sophisticated, we face the great challenge of how to model such data in order to draw valid statistical and biological conclusions. One important problem in genomic research is to relate these high-throughput genomic data to various clinical outcomes, including possibly censored survival outcomes such as age at disease onset or time to cancer recurrence. We review some recently developed methods for censored data regression in the high-dimension and low-sample size setting, with emphasis on applications to genomic data. These methods include dimension reduction-based methods, regularized estimation methods such as Lasso and threshold gradient descent method, gradient descent boosting methods and nonparametric pathways-based regression models. These methods are demonstrated and compared by analysis of a data set of microarray gene expression profiles of 240 patients with diffuse large B-cell lymphoma together with follow-up survival information. Areas of further research are also presented
Elephant Movements and Human-Elephant Conflict in a Transfrontier Conservation Area
In this thesis I explore how elephant movements are impacted by human activity within the context of the proposed Kavango-Zambezi Transfrontier Conservation Area (KAZA TFCA) in southern Africa. Being a wide-ranging species, the movements of elephants could be an excellent indicator as to the success of TFCAs in supporting species persistence in an anthropogenic matrix. Understanding which areas beyond protected area boundaries are of heightened conservation importance can provide managers and governments with insights for the management of the elephant population of KAZA TFCA, and assist managers and governments in prioritising conservation efforts
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Human-Induced Trophic Cascades along the Fecal Detritus Pathway
Human presence and activity in tropical forest is thought to exert top-down regulation over the various ‘green-world’ pathways of plant-based foodwebs. However, these effects have never been explored for the ‘brown-world’ pathways of fecal-detritus webs. The strong effects of humans on tropical game mammals are likely to indirectly influence fecal detritivores (including Scarabaeine dung beetles), with subsequent indirect impacts on detrivore-mediated and plant-facilitating detrital processes. Across a 380-km gradient of human influence in the western Brazilian Amazon, we conducted the first landscape-level assessment of human-induced cascade effects on the fecal detritus pathway, by coupling data on human impact, game mammal and detritivore community structure, and rate measurements of a key detritus process (i.e. dung beetle-mediated secondary seed dispersal). We found evidence that human impact indirectly influences both the diversity and biomass of fecal detritivores, but not detritivore-mediated processes. Cascade strength varied across detritivore groups defined by species' traits. We found smaller-bodied dung beetles were at higher risk of local decline in areas of human presence, and that body size was a better predictor of cascade structure than fecal resource manipulation strategy. Cascade strength was also stronger in upland, unflooded forests, than in seasonally flooded forests. Our results suggest that the impact of human activity in tropical forest on fecal-detritus food web structure is mediated by both species' traits and habitat type. Further research will be required to determine the conditions under which these cascade effects influence fecal-detritus web function
Assessing the contribution of ecosystem services to human wellbeing: A disaggregated study in western Rwanda
AbstractLack of attention to social complexity has created a gap between current ecosystem service research and the kind of insights needed to inform ecosystem management in the tropics. To contribute to closing this gap, this study applies a methodology for exploring complex linkages between ecosystem services and human wellbeing. This builds on emerging frameworks for studying multiple dimensions of human wellbeing, drawing on Amartya Sen's capabilities approach to human development. The approach is applied to an empirical case study of three sites adjacent to native tropical forest in western Rwanda. The value of exploring social complexity in ecosystem services research is illustrated through its contribution to understanding a) different types of values; b) disaggregation of people; c) power relations and their influence on trade-offs; d) the importance of multiple land use types in the landscape; and e) changes and their drivers at multiple scales. The analysis reveals that the majority of services valued by forest-adjacent Rwandan inhabitants are not provided by tropical forests but by other habitats. We suggest that more integrated landscape governance may offer synergistic opportunities for conservation and development
Predator-prey interactions in anthropogenic landscapes
Tre av fire artikler er fjernet fra den digitale versjonen, grunnet uklarhet om rettigheter. De kan leses i den trykte versjonen./ Three out of four articles have been removed from the digital version due to copyright. They can be read in the printed version.Interaksjoner mellom rovdyr og byttedyr er basert på flere faktorer, inkludert habitat og rovdyrets jaktmodus. Innenfor menneskepåvirkede landskap kan mennesker omforme interaksjoner mellom rovdyr og byttedyr ved å påvirke deres tetthet, atferd og overlevelse gjennom aktiviteter som jakt, skogsbruk og arealbruk. I menneskepåvirkede systemer er jakt den viktigste dødsårsaken for mange byttedyr, men med tilbakekomsten av store rovdyr står nå byttedyr overfor ytterligere dødlighetsrisiko.
Målene med denne oppgaven var å 1) undersøke plasseringen av jegerdrepte og ulvedrepte elg i landskapet under og etter jaktsesongen og vurdere om det resulterte i kontrasterende eller overlappende spatio-temporære risikomønstre for elg; 2) undersøke elgers habitatvalg i forhold til fordelingen av jakt- og ulvpredasjonsrisiko i tid og rom; 3) undersøke dødeligheten til elgkalv sommer og vinter i forhold til risiko fra både mennesker og store rovdyr (ulver og brunbjørn), og klimatiske og miljømessige faktorer (produktivitet og snødybde); og 4) vurdere om ulvens tilbakekomst hadde forårsaket enten tetthets- eller atferdsutløste trofiske kaskader som involverte elg og deres viktigste fødeart, furu. For å gjøre dette har det Skandinaviske ulveforskningsprosjektet (SKANDULV) og GRENSEVILT-prosjektet innhentet lokaliseringer av elg drept av jegere og utstyrt både elg og ulv med Global Positioning System (GPS) halsbånd for å søke etter bytterester og innhente data om elgens habitatvalg om sommeren, høsten (dvs. jaktsesongen) og vinteren (dvs. etter jaktsesongen). I tillegg ble merkede elgkuer oppsøkt til fots i felt tre ganger i løpet av året (ved fødsel, ved starten av jaktsesongen og like før kalvenes spredning om vårenkalvespredning) for å telle antall kalver.
Spatiotemporale Den romlige og tidsmessige variasjonen for jakt og predasjonsrisiko var korrelert med ulike naturlige og menneskeskapte faktorer. Jaktrisikoen var høyest nær åpne områder (f.eks. hogstflater og myrer) og veier, samt områder med lav bygningstetthet og liten grad av ulendt terreng. Ulvpredasjonsrisiko varierte tidsmessig og var høyest nær hogstflater/ungskog, lenger unna myr og i områder med lav bygningstetthet i jaktsesongen. Etter jaktsesongen var ulvepredasjonsrisikoen fortsatt høyest nærmere hogstflater/ungskog og i områder med lav bygningstetthet, men også nær hovedveier og i mer ulendt terreng. Når jeg sammenlignet de romlige egenskapene til jeger- og ulvedrept elg, fant jeg motsatte risikomønstre fra jegere og ulv.
I løpet av jaktsesongen unngikk elgen områder med høy jaktrisiko på dagtid, mens habitatvalget deres ble ikke påvirket av jaktrisiko om natten. Etter jaktsesongen ble ikke elgens habitatvalg 6 påvirket av jaktrisiko verken på dag eller nattestid. Elg valgte områder med høy ulvepredasjonsrisiko både dag og natt under og etter jaktsesongen.
Elgkalvdødeligheten om sommeren varierte betydelig mellom år, men var ikke relatert til verken predasjon fra ulv eller bjørn, klimatiske eller miljømessige variabler. Om vinteren var kalvedødeligheten positivt korrelert til snødybde og flatehogst/ungskog med nærvær av ulv, men også til økt jaktrisiko.
Forekomst og tetthet av elg, samt beiteskader, var positivt korrelert til forekomst av ulv. Samlet sett var miljømessige og menneskeskapte faktorer viktigere for å forklare elgforekomst og beiteskader enn ulveforekomst. Selv om ulv ikke drepte elg tilfeldig i landskapet og at deres tilstedeværelse resulterte i en positiv korrelasjon mellom kalvedødelighet og visse landskapstrekk, oppdaget jeg ingen tegn til at elg unngikk områder eller perioder med høyere risiko. Følgelig ser det ut til at ulver ikke har fremkalt verken tetthets- eller atferdsutløste trofiske kaskader i det sør-sentrale Skandinavia.
Resultatene mine tilsier at mens både jakt- og predasjonsrisiko varierte i tid og rom, responderte elg bare på jakt, som utgjør en større, men også mer forutsigbar risiko enn ulv. I løpet av det siste århundret har menneskers jakttradisjon på den Skandinaviske halvøy funksjonelt erstattet predasjon av ulv og bjørn på elg. Med tilbakekomsten av ulv justerte jegerne sine jaktkvoter på elg for å kompensere for den additive dødeligheten fra ulv. Elgens atferdsjustering på jaktrisiko kan tilsi at mennesker kan forårsake både tetthets- og atferdsutløste trofiske kaskader i menneskeskapte landskap. Ulver fremkalte derimot ikke atferdsresponser hos elg, som tilsier at elgen unngår risikofylte steder i risikofylte tider, og utløste heller ikke kaskadeeffekter på lavere trofiske nivåer. Den reduserte tilgjengeligheten av matressurser om vinteren kan tvinge elgen til å velge habitater med bedre næringstilgang som samtidig er kombinert med en større risiko for ulvepredasjon (f.eks. flatehogst/ungskog). Derfor kan ulvens potensiale til å sette i gang trofiske kaskader bli dempet, eller til og med kansellert, av elgens behov for næringstilgang om vinteren.ABSTRACT: Predator-prey interactions are shaped by several factors, including landscape features and hunting modes of predators. Within anthropogenic landscapes, humans can reshape predator prey interactions by influencing the density, behaviour and survival of both predators and prey through activities such as hunting, forestry practices and land use. Understanding the role that humans play within ecological communities is becoming increasingly important as large carnivores are recolonizing parts of their historical ranges. In anthropogenic systems, harvest is the main mortality source for many ungulate prey populations, and with the return of large carnivores, ungulates now face mortality risk from multiple sources.
The objectives of this thesis were to: 1) assess the spatial attributes of hunter-killed and wolf (Canis lupus)-killed moose (Alces alces) during and after the hunting season and determine whether it resulted in contrasting or overlapping spatiotemporal patterns of risk for moose; 2) investigate habitat selection of moose in relation to the spatiotemporal distribution of hunting and wolf predation risk; 3) evaluate moose calf mortality during summer and winter in relation to risk from both humans and large carnivores (wolves and brown bears, [Ursus arctos]) and climatic and environmental variables (productivity and snow depth); and 4) assess whether the return of wolves had elicited either density- or behaviourally-mediated trophic cascades involving moose and their main browsing species, Scots pine. In order to do so, the Scandinavian Wolf Research Project (SKANDULV) and GRENSEVILT project obtained the locations of moose killed by hunters and fitted both moose and wolves with Global Positioning System (GPS) collars to search for kill sites and obtain data on moose habitat selection during summer, fall (i.e., the hunting season) and winter (i.e., after the hunting season). Additionally, female moose were approached three times during the year (at birth, at the onset of the hunting season and just before calf dispersal) from the ground to count the number of accompanying calves.
Spatiotemporal patterns of hunting and predation risk correlated to both environmental and anthropogenic features. Hunting risk was highest close to open spaces (e.g., clearcuts and bogs) and roads and in areas with low building density and low terrain ruggedness. Wolf predation risk varied temporally and was highest close to clearcuts/young forests, further away from bogs and in areas of low building density during the hunting season. After the hunting season, wolf predation risk was still highest closer to clearcuts/young forests and in areas of low building 4 density, but also close to main roads and in more rugged terrain. When comparing the spatial characteristics of hunter-killed and wolf-killed moose, I found contrasting risk patterns from hunters and wolves.
During the hunting season, moose avoided areas of high hunting risk during the day, while their habitat selection was not affected by hunting risk at night. After the hunting season, moose habitat selection was not influenced by hunting risk during the day or at night. Moose selected areas of high wolf predation risk during both day and night during and after the hunting season.
Moose calf mortality in summer varied significantly between years but was not related to predation, climatic or environmental variables. In winter, calf mortality correlated positively to snow depth and clearcuts/young forests in the presence of wolves and increased hunting risk.
Moose presence and abundance and browsing damage were positively correlated to the presence of wolves. Overall, environmental and anthropogenic features were more important in explaining moose presence and browsing damage than wolf presence. Although wolves did not kill moose randomly in the landscape and their presence resulted in a positive correlation between calf mortality and certain landscape features, I did not detect a behavioural response in moose consistent with the avoidance of places and times of higher risk. Consequently, wolves seem to not have elicited either density- or behaviourally-mediated trophic cascades in south-central Scandinavia.
My results indicate that while both hunting and wolf predation risk varied spatiotemporally, moose responded only to the stronger, more predictable mortality source: hunting. During the last century in Scandinavia, hunting has functionally replaced predation by wolves and bears on moose. With the return of wolves, hunters adjusted their harvest quotas on moose to compensate for the additive mortality of wolves. Because moose adjusted their behavioural response to hunting risk, this may indicate that humans might have the potential to trigger both density- and behaviourally-mediated trophic cascades within anthropogenic landscapes. On the other hand, wolves did not elicit behavioural responses in moose consistent with the avoidance of risky places during risky times, nor triggered cascading effects on lower trophic levels. The decreased availability of food resources during winter may force moose to select habitats with greater forage opportunities that are simultaneously coupled with a greater risk of wolf predation (e.g., clearcuts/young forests). Hence, the potential for wolves to initiate trophic cascades might be dampened, or even cancelled, by the need for moose to find optimal foraging places during winter
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Inter-sexual and inter-seasonal differences in the chemical signalling strategies of brown bears
The brown bear (Ursus arctos) is a species which, due to its solitary, dominance hierarchy social system and large home range, is thought to rely heavily on chemical signals as a means of communication. Through camera traps orientated towards bear ‘rub trees’ over a two-year period, we assessed the proportional contribution of scent marking in different seasons by different age sex classes, and gained insights into the role of chemical signalling in maintaining social structure. We found, during the breeding season (June-July), that both adult males (n=38 P1 year (n=11 P=0.003) scent marked trees significantly more often than expected, whereas lone adult females (n=7) and subadults (n=3) marked less than expected. Outside of the breeding season (August-October), adult males (n=70) marked in an expected proportion, females with cubs (all ages) marked significantly more than expected (n=71 P<0.001), and lone adult females (n=11) and subadults (n=15) marked less than expected. During both the breeding season (n=7 P=0.026) and the fall (n=11 P<0.001), adult females marked trees significantly less than their occurrence on bear trails would expect, as did subadults during the breeding season (n=3 P=0.026) but not during the fall (n=15). Adult males marked at significantly high frequencies both during and outside of the breeding season, potentially to communicate dominance between males. Supported by the low frequency of scent marking by subadults. We observed a total avoidance of bear trails containing active rub trees by females with cubs <1 year during the breeding season, a possible counterstrategy to sexually selected infanticide due to the strong male bias in scent marking during the breeding season. We hypothesize that scent marking in brown bears is taught by the mother, beginning with cubs <1 year outside of the breeding season at a relatively ‘safe’ time of year
Habitat Selection by Parturient and Post-parturient Adult Female Moose (Alces alces) on the Canadian Prairies
The expansion of moose into the agricultural landscape of Saskatchewan (i.e., farmland moose) has increased human-wildlife conflicts, raising questions about how to best manage them. To support decision making, I initiated a study on farmland moose reproductive success and habitat selection following parturition (i.e., birth of calves). In 2013 and 2014, adult female moose were captured between Saskatoon and Chamberlain, SK and fitted with Global Positioning System collars. Daily movement rates and clustering of locations were used to determine the date and location of parturition for 27 adult female moose from 2013 to 2015. The mean date of parturition was May 21. Moose were surveyed using Very High Frequency radio telemetry in June and September each year to visually determine the presence and number of calves. Of the pregnant females observed during calf surveys with 1 or 2 calves, twinning rates were 67% (n = 6/9) in June 2013 and 46% (n = 5/11) in June 2014. Habitat selection ratios indicated that wetland and riparian habitat, trees and shrubs, and cropland were selected the most strongly by female moose as parturition habitat, while pastures and forages, developed and native grassland habitat were avoided. Female moose selected parturition sites further away from roads. A resource selection function model was developed to quantify habitat selection by 15 female moose with young during the first 20 days post-parturition. During this period, adult female moose with young most strongly selected for wetland and riparian areas (β [95% CI] = 0.716 [0.485, 0.946]) and native grassland (β [95% CI] = 0.457 [0.329, 0.585]) and against oilseeds (β [95% CI] = –0.252 [–0.400, –0.103]). Predictive success of the top-ranked model, estimated from k-fold cross validation, was rs = 0.993 (SE = 0.001). The resource selection function indicates that only 10% of the area within the home ranges of parturient females is considered highly selected habitat with high probability of moose use, while 48% of the area has a low probability of use. These results demonstrate the importance of wetland habitat within cropland to female moose, during and shortly after giving birth
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