Parasitism in plants is often accompanied by a suite of morphological and physiological changes resulting in a condition known as the ‘parasitic reduction syndrome’. With changes including extreme vegetative reduction, frequently beyond any resemblance to its photosynthetic relatives, accompanied by significant losses of genes linked to photosynthesis, the study of parasitic plants can be challenging. Conopholis (Orobanchaceae) is a small holoparasitic genus distributed across eastern and southwestern North America and Central America. This genus has never been the subject of a molecular phylogenetic or morphometric analyses. In addition, very little is known of the relationships among populations and of their post-glacial history. To investigate the species limits and phylogenetic relationships in Conopholis, we conducted a comprehensive molecular phylogenetic study of the genus as well as a fine-scale morphometric study. Based on plastid and nuclear sequences, Conopholis was found to contain three distinct and well-supported lineages which have varying degrees of overlap with previously proposed taxa. The clustering and ordination analyses of the morphometric study corroborated the molecular data, demonstrating the morphological differentiation between the three lineages detected within Conopholis. A taxonomic re-alignment is proposed for the genus that recognizes three species, C. americana, C. panamensis, and C. alpina. To address genetic diversity and phylogeographic structure of C. americana in eastern North America, microsatellite markers were developed and characterized for the first time in this species. Using these newly generated markers along with sequences from the plastid genome, the persistence of a minimum of two glacial refugia at the last glacial maximum were inferred, one in Florida and southern Alabama and another in the Appalachian Mountains near the southern tip of Blue Ridge Mountains. The diversity seen across the southern Appalachian Mountains supports the hypothesis that populations derived from the southern and northern refugia come together in this area.

Parasitism in plants is often accompanied by a suite of morphological and physiological changes resulting in a condition known as the ‘parasitic reduction syndrome’. With changes including extreme vegetative reduction, frequently beyond any resemblance to its photosynthetic relatives, accompanied by significant losses of genes linked to photosynthesis, the study of parasitic plants can be challenging. Conopholis (Orobanchaceae) is a small holoparasitic genus distributed across eastern and southwestern North America and Central America. This genus has never been the subject of a molecular phylogenetic or morphometric analyses. In addition, very little is known of the relationships among populations and of their post-glacial history. To investigate the species limits and phylogenetic relationships in Conopholis, we conducted a comprehensive molecular phylogenetic study of the genus as well as a fine-scale morphometric study. Based on plastid and nuclear sequences, Conopholis was found to contain three distinct and well-supported lineages which have varying degrees of overlap with previously proposed taxa. The clustering and ordination analyses of the morphometric study corroborated the molecular data, demonstrating the morphological differentiation between the three lineages detected within Conopholis. A taxonomic re-alignment is proposed for the genus that recognizes three species, C. americana, C. panamensis, and C. alpina. To address genetic diversity and phylogeographic structure of C. americana in eastern North America, microsatellite markers were developed and characterized for the first time in this species. Using these newly generated markers along with sequences from the plastid genome, the persistence of a minimum of two glacial refugia at the last glacial maximum were inferred, one in Florida and southern Alabama and another in the Appalachian Mountains near the southern tip of Blue Ridge Mountains. The diversity seen across the southern Appalachian Mountains supports the hypothesis that populations derived from the southern and northern refugia come together in this area.

The diurnal movements of Florida manatees (Trichechus manatus latirostris) in warmwater refugia are poorly understood and these may prove critical in accurately estimating populations of these animals. Previous studies indicate that manatee populations in such refuges in Tampa Bay, FL, peak mid-day and decline towards evening when the animals leave to forage. This trend suggests that variation in the timing of aerial manatee population surveys may hamper accurate estimation of the true population size. Aerial survey counts are known to underestimate population size, yet the extent of the underestimation may be greater than expected. In this study data were collected over three seasons from land-based surveys monitoring the presence of manatees in the effluent canal from the Florida Power and Light electricity generating facility in Port Everglades, FL between 15 November and 31 March. My findings indicated there was no significant difference in the number of manatees observed during the seasons studied despite a significant difference in ambient water temperatures. There was a significant correlation in the number of manatees an observer can expect to see based on time of day with the trend indicating there are higher numbers of observable manatees in the morning compared to later in the day. This suggests that early morning aerial counts will more accurately reflect true manatee presence in the Port Everglades power plant. Photographs of individual manatees yielded a total of 58 animals with unique scaring patterns.

To account for the effects of climate change, management plans in the northeast need to incorporate climate adaptation. Conserving climate change refugia is one adaptation strategy. Climate change refugia are areas buffered by climate change that enable the persistence of valued physical, ecological, and cultural resources; preserving these areas could be a potential adaptation strategy. Using a translational ecology approach where researchers and managers from the National Park Service, US Geological Survey, the University of Massachusetts, and elsewhere worked together, we focused on identifying refugia for tree, herbaceous plant, mammal, and bird species in order to prioritize them for conservation action. Results predict shifts in distribution of habitats and species due to climate change, identifying areas to prioritize for invasive species treatment and other management actions. This study highlights priorities for future monitoring and data analysis, providing a model that can be replicated in other regions and motivate future research.

This thesis explores how Swedish farmers, who have chosen to farm with heritage plant varieties, motivate their choices and how they as a result of their choices view themselves as farmers. This is investigated against present and future challenges regarding food security and the loss of agricultural biodiversity and biocultural heritage, which, in order to be faced, will require a wider range of plants in cultivation. To find out why farmers make certain choices is vital if we are to make necessary structural changes within the agricultural sector. The farmers’ motives are broad and they are, based on the concept of hybridity, presented and analysed through the categories memory, identity and reciprocity. These motives are also closely linked to how they view themselves as farmers. The findings are further interpreted through the concept of biocultural refugia, which is a means of studying how certain places can harbour different species while simultaneously being an area for sustainable food production. In this thesis biocultural refugia represents how the respondents are part of creating and maintaining diversity within plant cultivation and its surrounding practices. This diversity will be required in order for agriculture to handle current challenges in a sustainable way.

How long has the extant flora been present in the Antarctic? Glaciological reconstructions propose that most areas in Antarctica were covered by thick ice sheets throughout the Last Glacial Maximum (LGM; ~22-18 kya) as well as previous glaciations, suggesting terrestrial life must have been extremely limited during these periods. In contrast, recent biogeographic and genetic studies support most extant groups of Antarctic terrestrial fauna having survived past glaciations in situ. However, studies on the origin and age of the Antarctic flora remain sparse. Applying population genetic, phylogeographic and divergence time analyses I assessed the global biogeography, origin and age of several abundant Antarctic moss species, including: four Polytrichaceae mosses, characterised by having bipolar distributions, the most common (~45% of species) distribution pattern amongst Antarctic mosses; the globally widespread moss Ceratodon purpureus; the bank-forming moss Chorisodontium aciphyllum, also known for its old sub-fossils in Antarctica and long-term viability from revival experiments; and, lastly, the genus Schistidium, the most species-rich moss genus in Antarctica, including many endemic species. Genetic analyses revealed evidence of long-term (multi-million year) survival of plants in Antarctica (several species of Schistidium, Ceratodon purpureus, and possibly Polytrichum juniperinum). However, evidence for a likely more recent (< 100 ky) arrival of Chorisodontium aciphyllum was also found. Some species revealed multiple separate dispersal events to the Antarctic, suggesting the region may be less isolated for spore-dispersed organisms than previously thought. Evidence for increased genetic diversity in the northern maritime Antarctic compared to other regions point at it including potential refugial areas. Furthermore, genetic patterns revealed geographic features that enable and limit the connectivity of bryophytes globally as well as in Antarctica. This study suggests that, despite the harsh polar climate during glaciation periods, many bryophytes have had a much longer presence in Antarctica than previously thought.

Against the background of past, recent and future climate change, the present thesis addresses elevational shifts of alpine treelines in the Swedish Scandes. By definition, treeline refers to the elevation (m a.s.l.) at a specific site of the upper trees of a specific tree species, at least 2 m tall. Based on historical records, the first part of the thesis reports and analyzes the magnitude of treeline displacements for the main trees species (Betula pubescens ssp. czerepanovii, Picea abies and Pinus sylvestris) since the early 20th century. The study covered a large and heterogeneous region and more than 100 sites. Concurrent with temperature rise by c. 1.4 °C over the past century, maximum treeline advances of all species amount to about 200 m. That is virtually what should be predicted from the recorded temperature change over the same period of time. Thus, it appears that under ideal conditions, treelines respond in close equilibrium with air temperature evolution. However, over most parts of the landscape, conditions are not that ideal and treeline upshifts have therefore been much smaller. The main reason for that discrepancy was found to be topoclimatic constraints, i.e. the combined action of geomorphology, wind, snow distribution, soil depth, etc., which over large parts of the alpine landscape preclude treelines to reach their potential thermal limit. Recorded treeline advance by maximum 200 m or so over the past century emerges as a truly anomalous event in late Holocene vegetation history. The second part of the thesis is focused more on long-term changes of treelines and one specific and prevalent mechanism of treeline change. The first part of the thesis revealed that for Picea and Betula, treeline shift was accomplished largely by phenotypic transformation of old-established stunted and prostrate individuals (krummholz) growing high above the treeline. In obvious response to climate warming over the past century, such individuals have transformed into erect tree form, whereby the treeline (as defined here) has risen. As a means for deeper understanding of this mode of positional treeline change, extant clonal spruces, growing around the treeline, were radiocarbon dated from megafossil remains preserved in the soil underneath their canopies. It turned out that Picea abies in particular may attain almost eternal life due to its capability for vegetative reproduction and phenotypic plasticity. Some living clones were in fact inferred to have existed already 9500 years ago, and have thus persisted at the same spot throughout almost the entire Holocene. This contrasts with other tree species, which have left no living relicts from the early Holocene, when they actually grew equally high as the spruce. Thereafter they retracted by more than 300 m in elevation supporting that also on that temporal scale, treelines are highly responsive to climate change. The early appearance of Picea in the Scandes, suggests that Picea “hibernated” the last glacial phase much closer to Scandinavia than earlier thought. It has also immigrated to northern Sweden much earlier than the old-established wisdom. The experiences gained in this thesis should constitute essential components of any model striving to the project landscape ecological consequences of possible future climate shifts.

The Guiana Shield is a sub-region of Amazonia, one of the richest areas on earth in terms of species number. It is also one of the most pristine areas and is still largely unexplored. Species number, distribution, boundaries and their evolutionary histories remain at least unclear but most of the time largely unknown. This is the case for most Anurans, a group which is recognized as threatened globally and is disappearing even from pristine tropical forests. Given the pace of forest destruction and the growing concerns about climate change it is urgently necessary to obtain a better estimate of regional biodiversity in Amazonian frogs as well as a better understanding of the origin and distribution of Anuran diversity. Furthermore, given their sensitivity to climatic conditions, amphibians are a good model to investigate the influence of paleoclimatic events on Neotropical diversification which was supposedly the driving force on biotic evolution during Pleistocene in the Guiana Shield. I first test species boundaries in two species Scinax ruber and Rhinella margaritifera. These species are widely distributed, abundant and largely recognized as species complexes. I used an original species delineation method based on the combined use of mitochondrial and nuclear DNA in phylogenetic and phylogeographic analyses. Phylogenetic analyses demonstrated the polyphyly of Scinax ruber and Rhinella margaritifera. These species consist of multiple lineages that may all merit species status. Conflicting signals of mitochondrial and nuclear markers indicated the possibility of ongoing hybridization processes. Phylogeographic analyses added further information in support of the specific status of these lineages. Our results highlight the utility of combining phylogenetic and phylogeographic methods, as well as the use of both mitochondrial and nuclear markers within one study. This approach helped to better understand the evolutionary history of taxonomically complex groups of species. The assessment of the geographic distribution of genetic diversity in tropical amphibian communities can lead to conclusions that differ strongly from prior analyses based on the occurrence of currently recognized species alone. Such studies, therefore, hold the potential to contribute to a more objective assessment of amphibian conservation priorities in tropical areas. Subsequently, I tested if these first results on cryptic species are generalisable, questioning what would potentially be a minimum estimate of the number of cryptic frog species in Amazonia and the Guiana Shield, using mtDNA with multiple complementary approaches. I also combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contra to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher genetic distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas. As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised. The Rhinella margaritifera complex is characterisized by the presence of many cryptic species throughout its wide distribution, ranging from Panama to Bolivia and almost entire Amazonia. French Guiana has long been thought to harbor two species of this group, though molecular data analysed in previous chapters indicated as many as five lineages. I tested whether morphological measurements are correlated or not with genetic data using discriminant analysis and if diagnostic characteristics among the previously determined lineages can be used to describe these new species. This is a novel integrative method which can lead to a facilitation of the description of cryptic species that have been detected by phylogenetic and/or phylogeographic studies. These analyses, combined with published data of other Rhinella species, indicated that two of these lineages represent previously unnamed species. Two of the remaining are allocable to R. margaritifera while the status of the fifth is still unclear because so far it is morphologically indistinguishable from R. castaneotica. Determining if codistributed species responded to climate change in an independent or concerted manner is a basic objective of comparative phylogeography. Species boundaries, histories, ecologies and their geographical ranges are still to be explored in the Guiana Shield. According to the refugia hypothesis this region was supposed to host a forest refugium during climatic oscillations of the Pleistocene but the causes and timing for this have been criticized. We investigated patterns of genetic structure within 18 frog species in the eastern Guiana Shield to explore species boundaries and their evolutionary history. We used mtDNA and nuclear DNA and complementary methods to compare the genetic diversity spatially and temporally. With one exception all the species studied diversified repeatedly within the eastern Guiana Shield during the last 4 million years. Instead of one Pleistocene forest refugium the Guiana Shield has probably hosted multiple refugia during late Pliocene and Pleistocene. Most of these Pleistocene refugia were probably situated on the coast of French Guiana, Amapà, Suriname and Guyana. This diversification likely resulted from forest fragmentation. Many species deserve taxonomic revisions and their ranges to be reconsidered. The local endemism of the Anuran fauna of the Guiana Shield is likely to be much higher and some areas consequently deserve more conservation efforts. Specifically I questioned whether major intraspecific diversification started before the Pleistocene and occurred within the Guiana Shield or ex situ. According to ecological characteristics of the species involved I will test different diversification hypotheses. The consequences on the diversity and the endemism of the Guiana Shield will be explored. My results demonstrate that we have been grossly underestimating local biological diversity in the Guiana Shield but also in Amazonia in general. The order of magnitude for potential species richness means that the eastern Guiana Shield hosts one of the richest frog fauna on earth. In most of the species studied high levels of mtDNA differentiation between populations call for a reassessment of the taxonomic status of what is being recognised as single species. Most species display deep divergence between eastern Guiana Shield populations and Amazonian ones. This emphasizes that the local endemism in the Guiana Shield of these zones is higher than previously recognized and must be prioritised elements taken into account in conservation planning. Nevertheless, a few other species appear widely distributed showing that widespread species do exist. This underlines the fact that some species have efficient dispersal abilities and that the frog fauna of the eastern Guiana Shield is a mixture of old Guianan endemic lineages that diversified in situ mostly during late Pliocene and Pleistocene and more recently exchanged lineages with the rest of Amazonia. Recognizing this strong historical component is necessary and timely for local conservation as these zones are likely to be irremediably modified in the near future.

The impact of invasive predators on native prey may depend on the availability and distribution of invader-free refugia across landscapes, if predators create demographic ‘sink’ populations in invaded patches, giving rise to source-sink dynamics in prey populations. Propagule pressure of immigrants dispersing from refugia (or sources) may consequently drive persistence in sink habitat, affecting predator-prey co-existence across the landscape. I studied whether introduced brown (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) create source-sink structuring in two native galaxiid fish species (Galaxias vulgaris and G. paucispondylus) in the rivers of the central South Island, New Zealand, and whether such dynamics affected the distributions of either species across river networks or “riverscapes”. Young-of-the-year (YOY) G. vulgaris recruitment was rare in trout-invaded streams and consistently high in trout-free streams. Thus, trout-free reaches appeared to act as sources in a river network, while the majority of the trout-invaded riverscape was a demographic sink (i.e., no local recruitment occurred). Surveys of YOY G. paucispondylus did not reveal trout-induced source-sink dynamics, although mesocosm predation experiments suggested both species were highly vulnerable to predation by large trout. Galaxias paucispondylus recruitment was highest in intermittently flowing streams that were marginal habitats for trout, suggesting indirect interactions between trout and habitat affect G. paucispondylus distribution. Network configuration of trout-free source populations affected the distribution of G. vulgaris, as galaxiids were excluded from small streams with high bed stability that were far from sources. The interaction between propagule pressure and habitat gradients in mediating effects of trout on G. vulgaris distributions indicates habitat characteristics affect predator-prey interactions in a spatially explicit manner. Furthermore, the outcome of predator-prey interactions should be able to be modelled using habitat data alone if habitat consistently mediates predator impacts. I developed a GIS-based spatial model to predict where trout would exclude G. vulgaris in river networks, based on stream size and distance to galaxiid source populations. The model was tested in three different riverscapes using fish occurrence patterns obtained from electrofishing surveys, and successfully predicted G. vulgaris exclusion by trout. This further demonstrates the importance of habitat configuration in driving interspecific interactions at the landscape scale. These findings suggest removing trout from small, stable tributaries to create new demographic sources could improve overall persistence of G. vulgaris across trout-invaded riverscapes. The galaxiid exclusion model should also be used to detect undiscovered trout-free source populations, and to aid in selecting streams for restoration of galaxiid populations through trout eradication.

Pollen records from southeastern Vancouver Island, British Columbia, show changes in vegetation and climate from the late Olympia Interstade through the Fraser Glaciation. This study provides important insights into phytogeographic patterns of Pacific Northwest flora, leads to an enhanced understanding of processes affecting present-day ranges of several plant taxa, and provides a historical perspective on the origin of coastal alpine ecosystems. Evidence for a previously unrecognized glacial advance in the region at ~21,000 14C yr BP, herein called the Saanich glacier, is provided. The results reveal widespread habitat and food sources suitable for the mega fauna that lived on southern Vancouver Island during the last glaciation. Vegetation during the Fraser Glaciation represented a mosaic of plant communities across a heterogeneous and productive landscape. Pollen spectra indicate that plant assemblages, dominated by Poaceae and Cyperaceae, were widespread. Similarities to tundra in northern Alaska and high elevation sites in British Columbia were detected. Vegetation varied geographically in the late Olympia (ca. 33,500-29,000 14C yr BP). Grassy uplands with scattered trees and local moist meadows occurred at Qualicum Beach under mesic and cool conditions, while cold and dry grass tundra prevailed at Skutz Falls. Increased non-arboreal pollen percentages at Qualicum Beach, 29,000 14C yr BP, reflect expansion of grassy meadows with diverse herbs under a cool and dry climate at the onset of the Fraser Glaciation. At Qualicum Beach between 25,160-24,190 14C yr BP, sedge wetlands were surrounded by open, dry uplands. Concurrently at Osborne Bay, Pinus-Picea-Abies-Poaceae parkland occurred. Dry and cold climate intensified as the Fraser Glaciation progressed after 24,000 14C yr BP and non-arboreal communities expanded. At Cordova Bay, cold and dry tundra or parkland in upland sites, and sedge wetlands on an aggrading floodplain are recorded. Sparse tree cover and grass-tundra surrounded a floodplain at Skutz Falls around 21,000 14C yr BP under cool and dry climate. Subalpine-like Picea-Abies-Pinus parkland and moist, species-rich grassland meadows occurred at McKenzie Bight at the same time. A sedge wetland occupied the site of deposition, and was periodically inundated as lake levels fluctuated. Upland grasslands at Cordova Bay are recorded between 21,600–19,400 14C yr BP, while local ponded areas developed on an aggrading floodplain at sea level. From 19,400-19,300 14C yr BP, parkland at Cordova Bay developed as climate moistened and warmed at the time of the Port Moody Interstade known from the Fraser Lowland. Abundant marine dinoflagellate cysts between 21,600–19,400 14C yr BP, reveal a high sea level stand and strong marine influence at Cordova Bay. Glacioisostatic depression of the crust on the east side of Vancouver Island is the most probable explanation. The presence of pollen-bearing glacio-lacustrine sediments at McKenzie Bight around 21,000 14C yr BP at ~93 m and contemporaneous isostatic crustal depression at Cordova Bay strongly suggest a major glacial body in the region at the same time as the Coquitlam advance in the Lower Mainland. Ice-free landscapes may have occurred on southern Vancouver Island through the Fraser glaciation beyond the Saanich glacier ice limits. / Graduate