Conservation genetics for endangered species is crucial in long-term conservation actions.Inbreeding depression and genetic diversity are main genetic parameters with relevance toconservation. The Iberian lynx was by 2002 the most endangered felid in the world. Manyconservation programs have been carried out during the last 20 years, greatly improving theoutlook of the species. There is a paucity of information on the genetic consequences of thereintroduction program thus far. In the following research study, the most endangered Iberianlynx population, the Doñana population, is assessed to determine its actual genetic status andevaluate the genetic consequences of translocations initiated in 2007. This was achieved by thereconstruction of the pedigree of the wild population, and molecular analysis based on genotypedata with the use of Single Nucleotide Polymorphisms (SNPs). The molecular parameterscalculated were inbreeding coefficients, ancestry and genetic diversity. Results show an increase ingenetic diversity and a decrease in inbreeding following translocations. Post translocationinbreeding was found and explained by ancestral classes the individuals belonged to. These resultslay foundation for the importance of the ongoing translocations within the population andemphasize the need in the coming years for the conservation efforts carried out so far.

The dissertation thesis deals with human aesthetic preference to other species and its anthropological and conservation aspect. The aesthetic preference to animal species has rarely been systematically studied before and quantitative analyses, especially on a fine taxonomic scale did not exist. On the other hand, it was known that attractive species often receive more support for their conservation. From these simple facts rose the idea to test human aesthetic preference to snake species (and consequently to species across major vertebrate taxa) and use this quantified preference to explain the conservation effort devoted to captive breeding worldwide (measured as size of zoo populations). We confirmed that the perceived attractiveness (preference and/or species' body size) succesfully predicts the size of zoo populations across mammal, bird and reptile taxa. On contrary, we found no effect of the IUCN listing of the species. To find out whether we work with Czech students' preference only or we may generalize to other populations, we carried out the same experiment to determine human preference to boas and pythons in eight cultures of five continents. Despite profound differences of the studied ethnics, we revealed a considerable agreement. Moreover, we found an agreement between pre-school...

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The follicle and its enclosed oocyte share intimate and critical communication that regulates folliculogenesis and produces a mature oocyte. Protein and RNA accumulated in the oocyte during oogenesis control fertilization and direct embryonic development until the embryonic genome activates. Most knowledge of mammalian oocyte biology has been derived from eutherian species. Marsupials deserve more detailed studies because they have a distinct reproductive biology that offers a unique perspective from which to consider mammalian reproduction. The oocyte biology of the tammar wallaby, Macropus eugenii, is the focus of research in this thesis. Cold storage, a simple method for transporting ovarian tissue, was evaluated using histological techniques and follicle culture to assess the structure and function of tammar ovarian tissue. In vitro techniques were used to examine and compare: -folliculogenesis in prepubertal and adult animals, - fertilization of in vivo and in vitro matured oocytes, - and embryo development in follicular and tubal oocytes. / Tammar ovaries were placed in cold storage (PBS at 4?C) for 24 or 48 hours. Necrotic changes were minimal in ovarian follicles after cold storage and preantral follicles isolated from ovarian tissue after cold storage grew by similar amounts as non-stored follicles when cultured for 4 days in vitro. Although the general morphology and growth of follicles are unaffected after cold storage for up to 48 hours, the viability of the oocyte is of prime importance. The next important stages of this study were to develop in vitro techniques for follicle culture and for oocyte maturation and fertilization for future assessment of oocytes after cold storage. / A defined (serum-free) culture system was developed to grow isolated preantral follicles from prepubertal and adult tammars. FSH promoted follicle growth and antrum formation in follicles from prepubertal tammars. Although FSH promoted growth in follicles from adult tammars, other factors present in serum were required for antrum formation. Therefore, once the hypothalmo-pituitary-gonadal axis is mature, hormones and growth factors modify the mechanism of antrum formation. Only follicles that developed an antrum in the presence of serum had granulosa and theca layers that had appropriately differentiated. While FSH stimulates follicle growth in vitro, more complex conditions are required to promote granulosa and theca differentiation. / Intra-cytoplasmic sperm injection (ICSI) was successfully used to compare fertilization of in vivo and in vitro matured oocytes as well as the development of mature oocytes collected from the ovary (surrounded by zona pellucida) or from the oviduct (surrounded by zona pellucida and mucoid coat). In vitro matured oocytes proceeded though the early stages of fertilization (e.g. sperm nuclear decondensation, pronuclear formation), but not syngamy. After sperm injection, in vivo matured oocytes cleaved as far as the 8-cell stage. Oocytes do not lose their ability to fertilize after acquisition of the mucoid coat, since tubal oocytes cleaved as far as the 8-cell stage after sperm injection. Follicular oocytes develop as far as the 5-cell stage after sperm injection, but embryos had a large cleavage cavity that hindered cell-cell contact. While the mucoid coat is not required for cleavage, it is important for appropriate cell-cell interaction and normal early development of the embryo. / This, the most detailed in vitro study of marsupial oocyte biology, has shown that there are many similarities in the biology of marsupial and eutherian oocytes but that the unique biology of marsupials offers a significant perspective on mammalian reproduction. This work also lays the foundation for the effective use of assisted reproductive techniques for conservation of Australia’s unique mammalian fauna.

The follicle and its enclosed oocyte share intimate and critical communication that regulates folliculogenesis and produces a mature oocyte. Protein and RNA accumulated in the oocyte during oogenesis control fertilization and direct embryonic development until the embryonic genome activates. Most knowledge of mammalian oocyte biology has been derived from eutherian species. Marsupials deserve more detailed studies because they have a distinct reproductive biology that offers a unique perspective from which to consider mammalian reproduction. The oocyte biology of the tammar wallaby, Macropus eugenii, is the focus of research in this thesis. Cold storage, a simple method for transporting ovarian tissue, was evaluated using histological techniques and follicle culture to assess the structure and function of tammar ovarian tissue. In vitro techniques were used to examine and compare: -folliculogenesis in prepubertal and adult animals, - fertilization of in vivo and in vitro matured oocytes, - and embryo development in follicular and tubal oocytes. / Tammar ovaries were placed in cold storage (PBS at 4?C) for 24 or 48 hours. Necrotic changes were minimal in ovarian follicles after cold storage and preantral follicles isolated from ovarian tissue after cold storage grew by similar amounts as non-stored follicles when cultured for 4 days in vitro. Although the general morphology and growth of follicles are unaffected after cold storage for up to 48 hours, the viability of the oocyte is of prime importance. The next important stages of this study were to develop in vitro techniques for follicle culture and for oocyte maturation and fertilization for future assessment of oocytes after cold storage. / A defined (serum-free) culture system was developed to grow isolated preantral follicles from prepubertal and adult tammars. FSH promoted follicle growth and antrum formation in follicles from prepubertal tammars. Although FSH promoted growth in follicles from adult tammars, other factors present in serum were required for antrum formation. Therefore, once the hypothalmo-pituitary-gonadal axis is mature, hormones and growth factors modify the mechanism of antrum formation. Only follicles that developed an antrum in the presence of serum had granulosa and theca layers that had appropriately differentiated. While FSH stimulates follicle growth in vitro, more complex conditions are required to promote granulosa and theca differentiation. / Intra-cytoplasmic sperm injection (ICSI) was successfully used to compare fertilization of in vivo and in vitro matured oocytes as well as the development of mature oocytes collected from the ovary (surrounded by zona pellucida) or from the oviduct (surrounded by zona pellucida and mucoid coat). In vitro matured oocytes proceeded though the early stages of fertilization (e.g. sperm nuclear decondensation, pronuclear formation), but not syngamy. After sperm injection, in vivo matured oocytes cleaved as far as the 8-cell stage. Oocytes do not lose their ability to fertilize after acquisition of the mucoid coat, since tubal oocytes cleaved as far as the 8-cell stage after sperm injection. Follicular oocytes develop as far as the 5-cell stage after sperm injection, but embryos had a large cleavage cavity that hindered cell-cell contact. While the mucoid coat is not required for cleavage, it is important for appropriate cell-cell interaction and normal early development of the embryo. / This, the most detailed in vitro study of marsupial oocyte biology, has shown that there are many similarities in the biology of marsupial and eutherian oocytes but that the unique biology of marsupials offers a significant perspective on mammalian reproduction. This work also lays the foundation for the effective use of assisted reproductive techniques for conservation of Australia’s unique mammalian fauna.

abstract: Species conservation requires an understanding of the habitats on which that species depends as well as how it moves within and among those habitats. Knowledge of these spatial and temporal patterns is vital for effective management and research study design. Bubbling Ponds Hatchery in Cornville, Arizona, supports a robust population of the northern Mexican gartersnake (Thamnophis eques megalops), which was listed as threatened under the Endangered Species Act in 2014. Natural resource managers are interested in understanding the ecology of gartersnakes at this site to guide hatchery operations and to serve as a model for habitat creation and restoration. My objectives were to identify habitat selection and activity patterns of northern Mexican gartersnakes at the hatchery and how frequency of monitoring affects study results. I deployed transmitters on 42 individual gartersnakes and documented macro- and microhabitat selection, daily and seasonal activity patterns, and movement distances. Habitat selection and movements were similar between males and females and varied seasonally. During the active season (March–October), snakes primarily selected wetland edge habitat with abundant cover and were more active and moved longer distances than during other parts of the year. Gestating females selected similar locations but with less dense cover. During the inactive season (November–February), snakes were less mobile and selected upland habitats, including rocky slopes with abundant vegetation. Snakes displayed diurnal patterns of activity. Estimates of daily distance traveled decreased with less-frequent monitoring; a sampling interval of once every 24 hours yielded only 53–62% of known daily distances moved during the active season. These results can help inform management activities and research design. Conservation of this species should incorporate a landscape-level approach that includes abundant wetland edge habitat with connected upland areas. Resource managers and researchers should carefully assess timing and frequency of activities in order to meet project objectives. / Dissertation/Thesis / Masters Thesis Applied Biological Sciences 2017

Place-based biological conservation planning and recovery delineates “places” – spatial extents with favourable conditions for the recovery and management of multiple species simultaneously. Places represent geographic areas where constituent species are more likely to benefit from a specific set of recovery and management actions. Currently, place-based conservation planning is focused on prioritizing already-identified places. Findlay and McKee (2016) propose an approach to identify and delineate places by grouping geographical units based on species-at-risk (SAR) co-localization in (a) geographical, and (b) threat space. The following research is a practical application of the Findlay-McKee Methodology (FMM), using southern Ontario as a case study. I develop a parameterized algorithm to operationalize the design principles laid out in the FMM. I first define metrics to characterize the variation in SAR overlap and the degree to which sets of SAR share common threats. Next, I explore how the spatial extent of places (place size) changes as a function of tolerance for dissimilarity in both measures. The case study allowed me to evaluate the benefits and limitations of the FMM. I conclude that the FMM has the potential to be a defensible method for characterizing places based on SAR community overlap and inter-species threat similarity. However, the FMM’s applicability is limited by the availability of datasets at an appropriate resolution for analysis; uncertainty in selecting appropriate thresholds of tolerance for dissimilarity; and the criteria used to designate seed planning units. Given the increasing popularity of multi-species and ecosystem level recovery and conservation management, developing an efficient and effective process to guide place selection is crucially important. I recommend further research focus on empirically determining the number of places in a planning region and identifying at what tolerance thresholds places lose their ability to delineate areas where a comparatively small number of recovery actions will confer widespread benefits.

El tomate nativo peruano forma parte de la agrobiodiversidad del Perú, actualmente su conservación y producción la llevan a cabo los agricultores, quienes lo acogen como parte de sus otros cultivos luego de que las semillas de estas especies de tomate nativas caen en sus chacras o huertos. La preocupación que se tiene es que debido a la falta de cultivo y a las condiciones climáticas del Perú estas no se conserven adecuadamente. Es por lo que, a raíz de esta problemática, se desarrolló una investigación de tipo experimental, mediante la implementación de un Sistema IoT, con el fin de conservar mejor estas especies en un ambiente que ofrezca mayor control y monitoreo en tiempo real. Este consistió en el desarrollo de un circuito el cual fue colocado dentro de la Greenhouse, el cual tenía conectado sensores y actuadores, este emitía los datos captados por los sensores y el estado de los actuadores hacia un aplicativo móvil. Este proyecto se realizó con un cultivo de 5 ejemplares de Solanum lycopersicum variedad Cerasiforme, con el cual se obtuvo un rendimiento mayor de un 4.17% por parte del grupo experimental. / The Peruvian native tomato is part of the agrobiodiversity of Peru, currently its conservation and production is carried out by farmers, who welcome it as part of their other crops after the seeds of these native tomato species fall on their farms or orchards. The concern is that due to the lack of cultivation and the climatic conditions of Peru, these are not properly preserved. That is why, as a result of this problem, an experimental type of research was demonstrated, through the implementation of an IoT System, in order to conserve better species in an environment that offers greater control and monitoring in real time. This will consist of the development of a circuit which was placed inside the Greenhouse, which had sensors and actuators connected, this would emit the data captured by the sensors and the status of the actuators to a mobile application. This project was carried out with a culture of 5 specimens of Solanum lycopersicum variety Cerasiforme, with which a yield greater than 4.17% was obtained by the experimental group.

Bumblebees are ecologically and economically important as pollinators, but some species are suffering severe declines and range contractions. In this thesis, three cryptic bumblebee species are studied to elucidate differences in their distribution, ecology and population genetics. As a result of their high morphological similarity, very little is known about the lucorum complex species: B. lucorum, B, cryptarum and B. magnus. In this study, their distributions across Great Britain were assessed using molecular methods, revealing that B. lucorum was the most abundant and most generalist of the three species, whereas B. magnus was the rarest and most specialised, occurring almost exclusively on heathland. Additionally, both B. magnus and B. cryptarum were more likely to be present at sites with cooler summer temperatures. Cryptic species represent interesting models to investigate the levels of niche differentiation required to avoid competitive exclusion. Characterising the niches of these species at a single site across the flight season revealed differences along three niche dimensions: temporal activity, weather sensitivity and forage-resource use. These species exhibited asymmetric niche overlap; a combination of ecological divergence and spatio-temporal heterogeneity may contribute to maintaining them in sympatry. Population genetic studies can be highly informative for understanding species ecology and for conservation management. The differences in habitat specialisation exhibited by these bumblebee species provide the opportunity to test conflicting hypotheses about links between dispersal and ecological specialisation: are habitat specialists selected to have low or high dispersal ability? Based on microsatellite analysis, the generalist B. lucorum had high levels of genetic diversity and little population structure across large spatial scales. The habitat specialist B. magnus had the lowest genetic diversity but similar levels of population differentiation to the moderate generalist, B. cryptarum. However, unlike B. cryptarum, B. magnus population differentiation was not affected by geographic distance, suggesting that this specialist species may maintain effective dispersal across large scales despite being restricted to a fragmented habitat. Bergmann’s rule is a well-known ecogeographic rule describing geographical patterns of body size variation, whereby larger endothermic species are found more commonly at higher latitudes. Ectotherms, including insects, have been suggested to follow converse Bergmann’s gradients, but the facultatively endothermic nature of bumblebees makes it unclear which pattern they should adhere to. This thesis reports caste-specific differences in body size between the three lucorum complex species in agreement with Bergmann’s rule: queens and males of B. cryptarum and B. magnus, which were found more commonly at higher latitudes and at sites with cooler temperatures, were larger than those of B. lucorum. Population genetic studies of invertebrates generally require the destruction of large numbers of individuals, which is often undesirable. Testing a variety of faecal collection and DNA extraction methods demonstrated that it is possible to obtain DNA of sufficient quality for genotyping from bumblebee faeces, without harming the individuals. This method would be valuable for studies of rare or declining bee species, for queens in reintroduction projects, and may be applicable to other arthropods. Overall this thesis contributes substantially to our knowledge of the ecology and population genetics of three important pollinator species. It provides data to inform species conservation, as well as understanding of ecosystem functioning and population dynamics. Furthermore, it successfully uses these cryptic species as a model to test several fundamental ecological theories.

<p dir="ltr">In a rapidly changing world, human actions and natural events are reshaping ecosystems and presenting new challenges for conservation efforts. Within this context, unraveling the recent ecosystem transformations and their implications on a fine scale is required. The impacts of such changes are not always sudden but often gradual and sometimes as a result of historical events. With the recent advancement in technologies, the resolution of information by genome sequences spans from millions of years ago (hindcasting) to future generations (forecasting). Aquatic ecosystems pose their own challenges when it comes to ecosystem changes and the types of data required to assess impact and help inform conservation efforts. My dissertation comprises three chapters focused on using genomic techniques to generate data valuable for the conservation and management of aquatic ecosystems. Each of the three chapters is a distinct manuscript in terms of scientific publications, where Chapter 1 has already been published, Chapter 2 has been submitted to a journal, revised, and is now awaiting publication, and Chapter 3 is in preparation for submission to a peer-reviewed journal. In Chapter 1, dietary DNA from harvested North American river otter (<i>Lontra canadensis</i>)<i> </i>was used to determine whether metabarcoding of stomach content could be used to identify fish prey species consumed. In Chapter 2, DNA sequencing of endangered pupfish species in the Tularosa Basin of New Mexico was studied; before my work, it was nominally comprised of a single species, the White Sands pupfish (<i>Cyprinodon tularosa</i>). The results indicate a rapid speciation event occurred within about the last ~5000 years, driven primarily by genetic drift. Chapter 3 extends Chapter 2 by assessing the dynamics of genomic diversity over space and time while evaluating the short-term evolutionary dynamics (~18 generations) of the two native pupfish populations. This temporal study aimed to determine if the extraordinarily rapid evolution over the last ~5000 years (observed in Chapter 2) could be detected over timescales more relevant to conservation and management efforts. Overall, this dissertation used genomic sequence data from metabarcoding of the COI gene region in the otter stomach content as well as pool sequencing and whole genome resequencing of pupfish to provide key biological insights into the conservation of these aquatic species. This dissertation also provides insights into avenues for further study and highlights the significant role that conservation genomics can play in the future. The findings presented in the three chapters are discussed within the context of species’ conservation and management.</p>