Today biodiversity is rapidly decreasing and an increasing number of threatened species live in modified and human dominated landscapes. Therefore it is essential to learn more about how species cope with the changes of their habitat. The focus of this study lies on a primate species, the critically endangered Javan slow loris (Nycticebus javanicus), endemic to the densely populated island of Java, Indonesia.  In cooperation with the Little fire face project in West Java, I used a step selection function (SSF) framework, to understand how landscape structure affects the movement of Javan slow lorises within a fragmented mountain-agroforest landscape of Cipaganti, West Java. To investigate the movement and fine scale habitat selection of slow lorises I used one hour locations of 6 radio-collared slow lorises. The habitat and vegetation of observed and random steps was investigated in multiple variables such as presence of food trees and signs of human disturbance. For the analysis I paired observed steps (1h relocations) with 3 random habitat locations and used a conditional logistic regression to parameterize the SSF, which represents the probability of a focal slow loris to select a given step as a function of the habitat and vegetation factors surveyed. In average the slow lorises travelled about 450 m each night and most frequently they used a step length of about 0 – 50 m. My result reveals that slow lorises fine scale habitat selection is positively influenced by the presence of trees and tree trunk cover (indirect increasing the canopy cover and connectivity). They are also to a high extent positively affected by the presence of a feeding tree species, Calliandra calothyrsus. Surprisingly slow lorises selected steps associated with a higher number of fields (fields may indicate an increased biodiversity within the location). The results also indicate that slow lorises are limited in their movement by the presence of fields or rivers, which indicates that slow lorises are negatively influenced in their movement by a declining ability to move and forage within Cipaganti. I found no significant differences between sexes in their distance travelled. The recommendation for future conservation of slow lorises in Cipaganti is to prevent further habitat loss and fragmentation through activities that protect or maintain the present suitable slow loris habitat. Further research is needed to increase the knowledge of these primates’ abilities to live in this modified landscape.

Life history traits affect the timing and pattern of maturation, reproduction, and survival during an organism’s lifecycle and are the major components influencing Darwinian fitness. Co-evolved patterns of these traits are known as life history strategies (LHS) and variation occurs between individuals, populations, and species. The polymorphisms underlying LHS are important targets of natural selection, yet the underlying genes and physiological mechanisms remain largely unknown. Mapping the genetic basis of a LHS and subsequently unraveling the associated physiological mechanisms is a challenging task, as complex phenotypes are often polygenic. However, in several systems discrete LHS are maintained within the population and are inherited as a single locus with pleiotropic effects. These systems provide a promising starting point for investigation into LHS mechanisms and this thesis focuses on one such strategy - the Alba polymorphism in Colias butterflies. Alba is inherited as a single autosomal locus, expressed only in females, and simultaneously affects development rate, reproductive potential, and wing color. Alba females are white, while the alternative morph is yellow/orange. About 28 of 90 species exhibit polymorphic females, though whether the Alba mechanism and associated tradeoffs are conserved across the genus remains to be determined. In this thesis I primarily focus on the species Colias croceus and integrate results from lipidomics, transcriptomics, microscopy, and genomics to gain insights to the proximate mechanisms underlying Alba and Alba’s evolution within the genus. Lipidomics confirm that, consistent with findings in New World species, C. croceus Alba females have larger abdominal lipid stores than orange, an advantage which is temperature dependent and arises primarily due to mobilized lipids. Gene expression data suggests differences in resource allocation, with Alba females investing in reproduction rather than wing color, consistent with previous findings in other Colias species. Additionally, I identify a morphological basis for Alba’s white wing color. Alba females from C. croceus, an Old World species, and Colias eurytheme, a New World species both exhibit a significant reduction in pigment granules, the structures within the wing scale that contain pigment. This is a trait that seems to be unique to Colias as other white Pierid butterflies have an abundance of pigment granules, similar to orange females. I also map the genetic basis of Alba to a single genomic region containing an Alba specific, Jockey-like transposable element insertion. Interestingly this transposable element​ is located downstream of BarH-1, a gene known to affect pigment granule formation in Drosophila. Finally, I construct a phylogeny using a global distribution of 20 Colias species to facilitate investigations of Alba’s evolution within the genus. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p>

Egg-laying hens coming from commercial hatchery go through hatchery procedures considered as stressful and engaging prolonged stress response in adult chickens. The aim of our study was to evaluate the impact of commercial hatching procedure on the affective state of chicks, on their short- and long-term memory and on their need for social reinstatement. To assess the affective state of the chicks we used a cognitive bias protocol integrating the ecological response of a chick to the picture of another chick, to an owl and to an ambiguous cue mixing features of both the chickand the owl pictures. Short-term memory was evaluated by using a delayed matching-to-sample experiment (with 10, 30,60 and 120 s delays), with conspecifics as sample stimuli. We assessed long-term memory with an arena containing multiple doors leading to conspecifics, in which a chick had to remember which door was open after a delay of one hour or three hours. Finally, we observed the need for social reinstatement through a sociality test arena allowing a chick to be more or less close to conspecifics. We found that chicks coming from commercial hatchery were in a depressive affective state compare to control group. Those chicks also showed higher need for social reinstatement and loss weight. No differences were found regarding short- and long-time working memory between the two groups, but the methods used during these experiments will be discussed. Studying how commercial procedures impact the cognition and more specifically the emotions and state of mind of chickens, is a necessary step forward into the understanding of farm animals’ welfare.

Dolphins use stereotyped, individually distinctive, frequency modulated whistles, referred to as signature whistles, in order to broadcast their identity. In this study, we trained six dolphins at Kolmården Zoo, Sweden, to be called over, either upon hearing their own signature whistle (SW) or upon hearing a biologically irrelevant ”trivial” sound (TS), with the aim to prove the Whistle caller concept. The Whistle caller concept is based on the fact that dolphins occasionally use other dolphins’ signature whistles in order to address specific group members and convene.  Our hypotheses were that (1) dolphins call-over trained using their SW would learn the behaviour faster than dolphins trained using TSs, and (2) dolphins trained with their SW would be able to discriminate between different SWs better than dolphins trained with a TS would be at discriminating between different TSs.  Three out of three dolphins were successfully call-over trained using their SW, and two out of three dolphins using their assigned TS. When discriminating between different sounds, two of the dolphins trained using their SW performed significantly better than one of the dolphins trained using a TS. However, there were large intra-group differences in the results, indicating that we cannot eliminate the possibility that these results stem from individual differences in these dolphins’ ability to learn new behaviours overall, rather than an understanding of the sounds they heard. We suggest that future studies focus on (1) male-female differences in discrimination success when applying the Whistle caller concept, (2) how the characteristics of the trivial sounds affect discrimination success, and (3) the option of calling more than one animal at a time by sending out several SWs in succession.

The recovering harbor seal population along the Swedish west coast has coincided with declining cod stocks. Although the cod stocks were primarily depleted by intense fisheries, some stakeholders argue that reduced seal populations could have direct, positive effects on the cod stocks. The outbreaks of Phocine distemper virus (PDV) in 1988 and 2002 when up to 66% of the harbor seals along the Swedish west coast died, could be viewed as natural experiments allowing for assessment of any positive impacts of reduced mortality from seal predation on cod abundance. I quantified removal from seal predation and fishery landings and analyzed correlations to cod abundance of different length classes. Analyses were conducted for a longer time- series, 1979-2019, reaching back to when removal from fisheries was substantially larger than that from seal consumption. I also analyzed the data with a more recent perspective, 2003-2019, starting after the later PDV outbreak when seal predation relative landing sizes has increased. During this period, fishery discard data is available and included in the models. Methods include graphical presentation, multiple linear regression analyses, and to expand the existing data on seal diet, I collected diet samples of harbor seal feces from two haul-outs in Skagerrak. No statistically significant, negative correlations between seal predation and cod abundance were found in any data set, hence, I cannot support the idea of harbor seals having an impact on cod abundance. Also, the significant correlations between cod abundance and landings were all positive. I argue that culling of seals cannot be motivated as a strategy to help cod recover, as this would jeopardize the persistence of the seal population rather than assuring cod stability.

Browsing patterns in large herbivorous mammals are complex and decisions regarding food items occur at different levels depending on internal or external factors such as energy requirements and available food sources. A broader understanding of the behavior of animals living in habitats of economic interests for humans enables human exploitation with as little impact as possible on the animals' habitats. In this study, individual moose (Alces alces) tracks in the snow were surveyed in a mountainous environment with spruce-dominated forest, to map out what was browsed in relation to what was available in forests of two age classes: young and older. The following hypotheses were made: (1) every potential tree a moose passes will not be browsed and the browsed trees will be browsed to different degrees, and (2) the amount of available forage and the amount of used forage will differ between young and older forest. The moose tracks were followed on skis or on foot and all trees within browsing distance along a transect of 50 meters were counted and signs of browsing were recorded. Control transects (without fresh tracks) were also surveyed in the same forest areas where moose tracks were found. The data showed a higher proportion of available trees in young forest (60%) compared to older forest (40%) (all trees along the track transects), and a higher proportion of browsed trees in young forest (26%) compared to older forest (17%) (excluding Norway spruce, Picea abies). Downy birch (Betula pubescens) was the most abundant tree (56%) and Scots pine (Pinus silvestris) the least abundant (&lt;1%). Only 20% of all available trees along the track transects were freshly browsed to some extent, and even among the more selected species no more than around 50% of all available trees were freshly browsed. In young forest, Eurasian aspen (Populus tremula), rowan (Sorbus aucuparia) and willow (Salix spp.) were the most selected by moose, while common juniper (Juniperus communis) was the least selected. In older forest, however, gray alder (Alnus incana) was the most selected, followed by willow and rowan, while downy birch was the least selected. No browsing on Ericaceous shrubs were recorded in any of the transects. The study underlines that many different factors influence moose browsing choices, but generally a varied diet is sought and forests of different age classes, not exclusively young forests, are used for winter foraging. / Betesmönster hos stora växtätande däggdjur är komplext och val kopplade till föda sker på olika nivåer beroende på inre och yttre faktorer så som energibehov och tillgänglig föda. En bredare förståelse om beteenden hos djur som lever i habitat där människan har ekonomiska intressen möjliggör mänsklig exploatering med så lite påverkan som möjligt på djurens livsmiljöer. I den här studien spårades individuella älgar (Alces alces) i snö i en fjällnära miljö med grandominerad skog för att kartlägga vad som betades i relation till vad som fanns tillgängligt inom två åldersklasser; ung och äldre skog. Jag ställde upp två hypoteser: (1) varje potentiellt födoträd som en älg passerar kommer inte att vara betat på och de betade träden kommer att vara betade i olika grad, samt (2) mängd tillgängligt foder och mängd nyttjat foder kommer skilja sig mellan ungskog och äldre skog. Älgspåren följdes på skidor eller till fots och alla träd inom betesavstånd längs en transekt om 50 meter räknades samt kontrollerades för bete. Även kontrolltransekter (utan färska spår) inventerades i samma skogsområden där älgspår återfunnits. Datan visade på en högre andel träd i ungskog (60%) jämfört med äldre skog (40%) (alla träd längs spårtransekterna), och en högre andel betade träd i ungskog (26%) jämfört med äldre skog (17%) (gran, Picea abies, undantaget). Glasbjörk (Betula pubescens) var det mest förekommande trädet (56%) och tall (Pinus silvestris) det minst förekommande (&lt;1%). Enbart 20% av alla tillgängliga träd längs spårtransekterna var färskbetade i någon mån, och även hos de högre selekterade arterna var inte mer än runt 50% av alla tillgängliga träd färskbetade. I ungskog var asp (Populus tremula), rönn (Sorbus aucuparia) och sälg (Salix spp.) högst selekterade, medan en (Juniperus communis) var lägst selekterad. I äldre skog var däremot gråal (Alnus incana) högst selekterad följt av sälg och rönn, medan glasbjörk var lägst selekterad. Inget bete på bärris noterades längs någon av transekterna. Studien understryker att många olika faktorer påverkar betesval hos älg, men att en varierad diet generellt eftersträvas och skogar av olika åldersklasser, inte enbart ungskogar, nyttjas till födosök vintertid.

Selection pressure is a constant force in evolution, pushing birds and their wings towards an optimal shape and structure, were increasing performance, and minimizing the costs is central. But even though the science of aerodynamics can provide calculations of the optimal construction for the wing in different situations this rarely directly correspond to what is observed in nature. Since the optima are not the same for all birds due to different specifications and ecology this optimum becomes harder to determine and different functions can even have different optima, resulting in selection conflict. In the genius of birds there is an immense variation between species and their wings in everything from size, shape, and function.  The aim of this study is to investigate how wing morphology over a large phylogeny of bird species correlates to migration and habitat/ecology. Many studies have been done focusing on the effect of migration on the wing morphology, and some have been done focusing on other parameters such as display or daily usage. But by including the bird’s ecology and habitat related information with migration and morphology and looking at the selection from a broad perspective, can we uncover something more? The morphology of the wing cannot provide a perfect optimum for all circumstances since they require different specifications. What then, has the largest impact on the wing’s morphology? And does the relative length of the tail provide any correlations with its habitat and performance?  1185 birds of 137 species were caught at Ottenby, Öland and information on age, weight, sex, and tail length was collected for each individual bird. Photographs were taken of the back of the bird with the left wing outstretched 90 degrees from the body and analyzed in ImageJ to calculate aspect ratio and wing loading. Data on migration distance, foraging behavior, diet, and habitat density was then added for each of the species. Mean values of all parameters was calculated on species level creating a strong dataset with 137 data points. The species mean values dataset was used to test the interspecific effects and the dataset with all individuals was used to test intraspecific effects. ANOVAs, ANCOVAs, correlations tests and random slopes mixed models were performed revealing significant connections between wing morphology, migration, and habitat density. Correlations could also be observed between wing morphology, diet, and foraging behavior. Habitat density revealed the highest correlation with wing morphology, demonstrating a greater significance than migration and the other parameters. Effects that at first sight looked significant could later be excluded as they turned out to be dependent on other variables. The study therefore also highlights the importance of including alternative parameters for reliable conclusions.

Incidental bycatch in gillnets is a substantial threat to small cetaceans. Using Acoustic Deterrent Devices, “pingers”, have successfully reduced bycatch of harbour porpoises in gillnets. However, seals can use pingers as “dinner-bells” to easier find gillnets in order to raid and destroy them, further aggravating the existing conflicts between seals and coastal fisheries. Therefore, in the present study, the efficiency of two alleged “seal-safe” pingers, an experimental Banana pinger “SSB” and a Future Oceans F70 pinger “FO”, in deterring harbour porpoises from the vicinity of gillnets and thereby reducing bycatch in commercial gillnet fisheries, was tested. This was done by deploying click detectors, “C-PODs”, recording Detection Positive Minutes per hour, at each end of gillnets, provided with the two pinger types or no pingers at all. Bycatch instances were recorded into logbooks by participating fishermen and verified using video footage from on-board video cameras. Results showed that video monitoring was a reliable method for verifying the number of bycatches of porpoises and seals, but not seabirds, recorded in the fishermen’s logbooks. The experimental SSB pingers and the FO pingers significantly reduced porpoise presence, measured as Detection Positive Minutes per hour in the vicinity of the nets, compared to gillnets without pingers. However, the sample size was too small to yield a significant result regarding the bycatch reducing efficiency and dinner bell effect of the experimental pingers. Nevertheless, bycatch trends suggest that pingers did in fact reduce porpoise bycatch. Although both successful, FO pingers were slightly more efficient in deterring porpoises than SSB pingers. The SSB pinger sounds had bigger directionality variations than the FO pinger, which may have affected its deterrent effects. Therefore, additional trials are needed to further investigate this aspect.

No description available.

Management of rare and threatened species requires an understanding of processes limiting population establishment and growth. The Large blue butterfly Phengaris arion needs two other organisms, the Thyme plant Thymus serpyllum and the ant genus Myrmica, for the completion of its life cycle. The large blue butterfly is very rare in Sweden and also declining in Europe, and both the large blue and Myrmica are red-listed and in need of protection. Studies conducted in Great Britain have suggested that a lack of suitable habitat with the presence of the host plant thyme and Myrmica limits the distribution of the large blue. A good environment for the butterfly is thus a habitat where all three organisms can exist. To examine whether vegetation structure and abundance of Thymus serpyllum and Myrmica ants are good predictors of the presence of the large blue in Sweden, I investigated sites where the butterfly has been observed or reportedly gone extinct in the last five years. I studied one site in the region of Stockholm, five sites in the Uppsala region, and 10 sites on the island of Gotland. At each site, I recorded an abundance of thyme and its flowering status, the presence of shrubs, trees, and open vegetation, and any observations of the large blue.  Areas with the large blue tended to have a higher abundance of thyme plants and a higher percentage of thyme flowers in bloom during my visit than areas without the large blue. The difference in abundance of shrubs and trees between sites with and without the butterfly was small. Areas with the large blue also tended to have shrubs and trees compared to areas without the large blue. Because the study species are rare and endangered, the number of sites with current and past occurrence is limited, which complicates the statistical analysis of factors influencing its distribution. However, the results indicate the importance of a high abundance of the host plant for the occurrence of the large blue, but also that the host plant is much more common than the butterfly. Ants of the genus Myrmica were observed at only two of eight sites with observations of the large blue.  This suggests that the method used to detect Myrmica ants was not efficient, or that the large blue is not critically dependent on Myrmica ants in Sweden. To conclude, the remaining populations of the large blue should be monitored and measures to improve habitat quality should be considered at sites where it has gone extinct. We can try to reintroduce species in areas where the species has previously existed with strong populations of the thyme and the ant. Create a similar reintroduction as the success story of the large blue butterfly in Great Britain.