Because of increasing frequency of bear sightings, vehicle collisions, and nuisance incidents in coastal South Carolina, the South Carolina Department of Natural Resources is developing a comprehensive black bear management plan. However, no reliable estimates of population abundance or density are available. I used genotypes of black bears determined from hair samples collected in Lewis Ocean Bay and Carvers Bay to estimate population abundance and density. I obtained hair samples from snares during 8 weekly sampling periods in 2008 and 2009. I used Huggins closed population models to estimate abundance and spatially explicit capture- recapture models to estimate density. Based on model averaging, black bear abundance was 30 (SE = 9.3) on Carvers Bay and 42 (SE = 5.4) on Lewis Ocean Bay. Model-averaged density was 0.037 bears/km2 (SE = 0.003) for Carvers Bay. For Lewis Ocean Bay, population densities were much higher: 0.307 bears/km2 (SE = 0.025). I extrapolated the density estimates to the upper coastal region of South Carolina, using logistic regression to weight density based on similarity of the regional landscape with the 2 study areas. Predicted bear densities were low throughout the coastal region but several areas centered on more productive habitats (e.g., Carolina Bays, pocosin) and public lands (e.g., Francis Marion National Forest, Lewis Ocean Bay) had high densities. I also sampled an area in North Carolina and assessed genetic structure among the 3 areas. Based on heterozygosity, genetic distance, and genetic assignment, I found no evidence of historic or recent barriers to gene exchange among the 3 sampled populations. However, demographic connectivity may be a concern for areas such as Lewis Ocean Bay, which is surrounded by highways and development. If the goal is to maintain current black bear densities in those areas, maintaining connectivity with other habitat areas and mitigating impacts of highways would be important. The regional map of potential black bear density may be useful to identify areas that should be surveyed for occupancy or where additional studies may be conducted (e.g., Francis Marion National Forest).

Complex interactions between topographic heterogeneity and steep gradients in climate and environmental conditions are commonly assumed to promote biotic diversification. Using tropical frogs as a model, I investigate the nature of these interactions that disrupt migration between populations, causing genetic divergence and speciation. I determine the role of several putative factors that affect gene flow (Euclidean distances, Least Cost Path (LCP) distances, topographic complexity, and elevation difference) and promote genetic structure (FST) between populations of three tropical Andean frog species. Moreover, I investigate, from an intraspecific perspective, whether montane frog species display on average larger genetic distances per kilometer relative to lowland species. Finally, I test if recent genetic divergence caused by topographic barriers to gene flow is paralleled by independent character systems such as acoustics and morphological traits in the high Andean frog Dendropsophus labialis. Even though the effect of geographic features on migration (and conversely, FST) was species-specific, LCP and Euclidean distances had the strongest effect on migration rate. Topographic complexity also reduced migration rate whereas elevation difference did not have an effect. I found that indeed highland species show larger genetic distances per kilometer between haplotypes than do lowland species. Also, genetic divergence is strongly associated with topographic heterogeneity, which is an intrinsic characteristic of montane regions. Finally, I found that acoustic variation in D. labialis diverges according to genealogical history, but external morphology does not follow this relationship. Stochastic processes due to genetic drift appear to be a better explanatory mechanism for the divergence in calls than adaptive variation. The strong and congruent divergence observed in acoustic and genetic characters indicates that these two groups correspond to morphologically cryptic parapatric species. Overall, the results of this study suggest some of the mechanisms that allow tropical mountains to promote intraspecific genetic divergence. The combined effect of ridges (promoting allopatric differentiation) and environmental gradients across elevation (promoting parapatric differentiation) are effective forces that are present mostly in highland biomes. Unfortunately, such biomes are critically threatened by habitat destruction and climate change, possibly more than any other biome on earth. / text

Because American black bears (Ursus americanus) are an important game species in Arizona and are endangered in México, an understanding of the population structure, gene flow, and connectivity are important for effective management. Black bears inhabit coniferous and broadleaf deciduous woodlands in southern Arizona and northern México, usually in sky islands (sky islands are mountains that rise from the desert and are isolated from each other). Because a single sky island is too small to support a viable bear population, black bears move through desert lowlands to reach other sky islands. My objective was to assess genetic structure, connectivity, and conservation implications for sky island black bears in southern Arizona and northern México. I addresses 4 components of bear ecology and genetics: a literature review of genetic information available for black bears in North America; the use of 2 mitochondrial DNA genes (Control Region and ATP synthase protein 8) to study the phylogenetic relationship of black bears from the sky islands of southern Arizona and northern México relative to all North America; the use of 10 microsatellite loci to detect the current genetic structure of black bears in the sky islands in Arizona and northern México; and the use of noninvasive samples collected from the field to determine bear density and population size for black bear in Sierra San Luis, Sonora, México. These studies provide information that can be used by biologists, land managers, and others to assist in the conservation of black bears and their habitat.

Understanding dispersal and gene flow in human-modified landscapes is crucial for effective conservation. Seed dispersal governs colonization, recruitment, and distribution of plant species, whereas both pollen and seed dispersal determine gene flow among populations. This PhD thesis tests the effect of rotational shepherding on seed dispersal and gene flow in fragmented calcareous grasslands. Calcareous grasslands (Gentiano-Koelerietum pyramidatae vegetation) in Central Europe are semi-natural communities traditionally used for rotational grazing that experienced a decline of plant species during the 20th century due to abandonment of shepherding. This PhD profits from a management project started in 1989 in Bavaria, Germany to reconnect previously abandoned calcareous grasslands in three non-overlapping shepherding systems. Two vegetation surveys in 1989 and 2009 revealed colonizations in previously abandoned grasslands reconnected by shepherding. First, I propose a comprehensive approach to identify determinants of community-level patch colonization rates based on 48 habitat specialist plants by testing competing models of pre-dispersal and dispersal effects and accounting for post-dispersal effects. Mean source patch species occupancy in 1989, and structural elements in focal patches related to establishment explained community-level patch colonization rates. Secondly, by adapting the community analysis to all 31 individual species of the same community with sufficient data, I corroborate the role of shepherding to support dispersal for a range of species, even if they lack seed morphological traits related to zoochory. Thirdly, for the habitat specialist Dianthus carthusianorum, I genotyped 1,613 individuals from 64 populations at eleven microsatellites to test the effect of dispersal by sheep on spatial genetic structure at the landscape scale. Genetic distances between grazed patches of the same herding system were related to distance along herding routes, whereas ungrazed patches showed isolation by geographic distance. Lastly, within individual grassland patches, shepherding significantly decreases the degree of relatedness among neighboring individuals (kinship structure) and increases genetic diversity. My thesis contributes towards understanding the effects of zoochory on spatial dynamics in plant populations across scales.

Understanding dispersal and gene flow in human-modified landscapes is crucial for effective conservation. Seed dispersal governs colonization, recruitment, and distribution of plant species, whereas both pollen and seed dispersal determine gene flow among populations. This PhD thesis tests the effect of rotational shepherding on seed dispersal and gene flow in fragmented calcareous grasslands. Calcareous grasslands (Gentiano-Koelerietum pyramidatae vegetation) in Central Europe are semi-natural communities traditionally used for rotational grazing that experienced a decline of plant species during the 20th century due to abandonment of shepherding. This PhD profits from a management project started in 1989 in Bavaria, Germany to reconnect previously abandoned calcareous grasslands in three non-overlapping shepherding systems. Two vegetation surveys in 1989 and 2009 revealed colonizations in previously abandoned grasslands reconnected by shepherding. First, I propose a comprehensive approach to identify determinants of community-level patch colonization rates based on 48 habitat specialist plants by testing competing models of pre-dispersal and dispersal effects and accounting for post-dispersal effects. Mean source patch species occupancy in 1989, and structural elements in focal patches related to establishment explained community-level patch colonization rates. Secondly, by adapting the community analysis to all 31 individual species of the same community with sufficient data, I corroborate the role of shepherding to support dispersal for a range of species, even if they lack seed morphological traits related to zoochory. Thirdly, for the habitat specialist Dianthus carthusianorum, I genotyped 1,613 individuals from 64 populations at eleven microsatellites to test the effect of dispersal by sheep on spatial genetic structure at the landscape scale. Genetic distances between grazed patches of the same herding system were related to distance along herding routes, whereas ungrazed patches showed isolation by geographic distance. Lastly, within individual grassland patches, shepherding significantly decreases the degree of relatedness among neighboring individuals (kinship structure) and increases genetic diversity. My thesis contributes towards understanding the effects of zoochory on spatial dynamics in plant populations across scales.

Characterizing the population genetic structure of a species can provide insight into isolating effects of local adaptation and genetic drift, and homogenizing effects of gene flow. The relative interplay between gene flow and genetic drift can indicate whether multiple conservation units are needed to preserve biodiversity. Baja California, Mexico is a biodiversity hotspot where many individuals are genetically differentiated from conspecific individuals breeding elsewhere. Cassin’s auklet (Ptychoramphus aleuticus), a zooplanktivorous seabird, breeds in colonies along the Pacific coast of North America. One subspecies, P. a. australe, is described from Baja California and another, P. a. aleuticus, is described from the rest of its range to the Aleutian Islands, Alaska. Many of the colonies throughout its range have been declining in numbers likely as a result of decreases in food availability in cold-water upwellings along the coast. The mitochondrial control region and eleven nuclear microsatellites were analyzed using programs based on coalescent and Bayesian theory to determine how the southern subspecies compares genetically to the main subspecies. First, population genetic structure was characterized throughout Cassin’s auklet’s breeding range using pairwise genetic differentiation indices, hierarchical analysis of variance, statistical parsimony and Bayesian clustering methods. The two subspecies were genetically differentiated but individuals breeding in the Channel Islands were more genetically similar to P. a. australe individuals. Population genetic differentiation was not evident within the two genetic groups. Second, gene flow between the two genetic groups was estimated using coalescent and Bayesian methods. Significant gene flow was estimated from the northern group (Aleutian Islands to Southeast Farallon Islands) into the southern group (Channel Islands to San Benito Island) but not from the southern group into the northern group since the time of divergence, possibly as a result of the non-breeding distribution. Results show that the two genetic populations diverged recently and the populations have experienced a recent population change in size. Restrictions in home range and foraging range may cause population genetic differentiation, resulting in two distinct management units. Genetic differentiation of the southern population provides support for Baja California and southern California being a biodiversity hotspot. / Thesis (Master, Biology) -- Queen's University, 2012-09-28 14:02:24.007

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Genetic diversity is a fundamental attribute that contributes to a species evolutionary survival. In recent times, conservation managers have recognized the need to preserve genetic diversity of declining species, and have also acknowledged the utility of genetic markers for describing genetic and ecological relationships within and among populations. Information obtained from genetic studies can be used in conjunction with information on population demography, land use patterns and habitat distribution to develop effective management strategies for the conservation of species in decline. The wallum froglet, Crinia tinnula, is one of Australia's smallest habitat specialist anurans. In recent years there has been a dramatic decrease in population numbers of this species. The habitat to which C.tinnula is endemic ('wallum' habitat) is restricted to low coastal plains along the southeast Queensland and northern New South Wales coastline. As human populations in this region expanded, the coastal areas have undergone significant development and large areas of wallum habitat have been cleared. The effect has been to convert once largely continuous patches of coastal heathland in to a matrix of small habitat patches within an area undergoing rapid urban expansion. This study aimed to document levels and patterns of genetic diversity and to define the population structure of C.tinnula populations within southeast Queensland, with the objective of defining possible conservation management units for this species. Results from 12S and COI mitochondrial markers clearly showed that two distinct evolutionary lineages of C.tinnula are present within southeast Queensland. The high level of divergence between lineages and strict geographic partitioning suggests long term isolation of C.tinnula populations. It is hypothesized that ancestral C.tinnula populations were once confined to wallum habitat refugia during the Pliocene resulting in phylogeographic delineation of 'northern' and 'southern' C.tinnula clades. Populations within each geographic region show evidence of range contraction and expansion, with subsequent restricted gene flow. Levels of genetic diversity appear, largely, to be the product of historical associations rather than contemporary gene flow. A revision of the current systematics of C.tinnula is required to ensure that discrete population groups are recognized as distinct evolutionary lineages and will therefore be protected accordingly.

Made available in DSpace on 2014-06-11T19:30:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-11-04Bitstream added on 2014-06-13T21:01:18Z : No. of bitstreams: 1 suganuma_ch_dr_jabo.pdf: 2851427 bytes, checksum: 03ed93e6b51f4af5d916613162e4b58b (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O presente trabalho teve como objetivo principal ampliar o conhecimento sobre a estrutura genética e obter informações para a conservação de pacu (Piaractus mesopotamicus Holmberg, 1887), provenientes de populações selvagens dos rios da Bacia do Alto Paraguai. Esta espécie possui grande valor comercial e imenso potencial para exploração em pisciculturas. Os marcadores moleculares do tipo microssatélite utilizados neste estudo, resultaram em muitas informações sobre a estrutura populacional desta espécie, permitindo uma possível caracterização dos bancos genéticos para esta espécie. Exemplares provenientes de nove sub-bacias do Pantanal Matogrossense foram coletados para a realização da extração de DNA visando à análise do material genômico. Para isto, foram retirados pequenos fragmentos de nadadeira de cada indivíduo. A amplificação dos locos microssatélites foi realizada num termociclador de PCR utilizando oligonucleotídeos marcados com fluorescência, conforme descrito na literatura. A genotipagem foi realizada no seqüenciador automático MegaBACETM 1000 (Amersham Biosciences), pertencente ao Centro de Estudos do Genoma Humano da Universidade de São Paulo. Os tamanhos dos alelos obtidos foram organizados para a montagem das matrizes de dados que foram submetidas aos programas computacionais para verificar a variabilidade genética nas populações. Os parâmetros que permitiram a determinação da diversidade genética intra e interpopulacional foram o número de alelos por loco, riqueza alélica, heterozigosidade observada e esperada, equilíbrio de Hardy Weinberg, índices Fst e Rst, análise de variância molecular (AMOVA), índice de fixação, desequilíbrio de ligacão e o número de migrantes. Também foi feita uma análise bayesiana para verificar a estrutura populacional e um dendrograma foi gerado a partir da matriz de distância baseada... / This work aimed to obtain information about the genetic structure of pacu (Piaractus mesopotamicus Holmberg, 1887), from wild populations of Alto Paraguai Basin Rivers. This specie has a greatly commercial importance, with huge potential for hatcheries. The pacu has a wide distribution in the Prata Basin, formed by Paraguay, Paraná and Uruguay rivers and their tributaries Microsatellites markers offer relevant information about this specie, allowing the characterization of genetic stocks. Individuals from nine sampling sites in the Pantanal Matogrossense were analysed in this study. DNA extraction methods did not required killing the samples, we used fin clippings from each individual. The amplification of microsatellites loci was carried out via polymerase chain reaction (PCR) using oligonucleotide marked with fluorescent labels. The amplified fragments were analysed on the automatic DNA sequencer MegaBACETM 1000 (Amersham Biosciences), belonged to Centro de Estudos do Genoma Humano from Universidade de São Paulo. Allele sizes were organized in an input file that was submitted statistical analysis to verify the genetic variability of populations. The parameters used to estimate the genetic diversity intra and interpoulation were number of allele per locus, allele richness, observed and expected heterozygosities, Hardy Weinberg equilibrium, molecular variance analyses (AMOVA), fixation index, linkage disequilibrium and gene flow. Bayesian estimates were used to verify the populacional structure and a dendogram was calculated by the distances matrix based on chord distances values. The results showed no population structuring and intense gene flow. The most probable causes are the hight migratory capacityof this fish and the climatic and geographic characteristics of the Pantanal Matogrossense.

L’émergence et la ré-émergence de maladies que nous connaissons depuis ces cents dernières années représentent une véritable crise sanitaire en grande partie due aux perturbations anthropiques qui modifient les écosystèmes et les interactions entre les parasites et leurs hôtes. La prévention et le contrôle des maladies infectieuses nécessitent la compréhension de leur dynamique dans l’ensemble des compartiments dans lesquels elles circulent. Parmi ces maladies, la fasciolose est une maladie particulièrement sensible aux changements liés à l’Homme. Cette zoonose causée par le parasite Fasciola hepatica, est communément reconnue comme un problème vétérinaire, mais aussi de santé publique, dans certaines régions du monde. Notre étude vise à comprendre la dynamique de circulation et les risques d'émergence de la fasciolose dans un contexte de forte anthropisation. Il s'agit (1) d'étudier la dynamique de l’hôte intermédiaire, un mollusque de la famille des lymnaieidae. (2) de comprendre la dynamique et la diversité du parasite entre et au sein de ses différents compartiments hôtes définitifs. Ces travaux ont été menés sur le territoire camarguais sur le domaine de la Tour du Valat, nous permettant d’avoir accès aux hôtes définitifs, sauvages (ragondins et sangliers), domestiques (taureaux traités et non traités) et à l’hôte intermédiaire, Galba truncatula appelé communément limnée tronquée. Dans un premier temps, nous avons caractérisé la végétation des habitats favorables à la présence du mollusque et nous avons trouvé que les mares semblaient être des zones présentant un risque plus important que les canaux d’irrigation pour la transmission de la fasciolose. Puis, nous nous sommes intéressée à l’influence des habitats sur la dynamique de G. truncatula par des approches de génétique des populations. Nos résultats ont permis de montrer que la permanence des habitats et la connectivité influencent le mode de reproduction, la structuration des populations et la dispersion des limnées en Camargue. Dans un second temps, nous avons étudié la dynamique et la circulation du parasite au sein du compartiment hôte définitif. Nos résultats de la génétique des populations du parasite chez les hôtes définitifs, nous ont indiqué qu’il existait sur notre site d’étude plusieurs sites de transmission constituant un seul grand foyer global. Par ailleurs, l’étude de la circulation du parasite entre les hôtes définitifs suggère le rôle des sangliers dans la dispersion de la maladie et le rôle des ragondins dans le maintien du cycle de la fasciolose. Cette étude met en évidence l’intérêt de mener des études à long terme et l’importance de prendre en compte tous les compartiments impliqués pour comprendre l’épidémiologie d’une maladie. Elle souligne également le rôle des activités humaines et de l’écosystème dans la dynamique de la fasciolose. Le but final de cette étude est de proposer une gestion intégrée adaptée au contexte camarguais afin de limiter l’impact sanitaire de la fasciolose mais aussi des autres maladies liées à l’élevage dans cette région. / The emergence and re-emergence of diseases encountered over the last hundred years represent a real health crisis largely due to anthropic disturbances that affect the ecosystems as well as the interactions between parasites and hosts. The prevention and control of emerging infectious diseases require an in-depth understanding of their dynamics in all the compartments in which they occur. Among these diseases, Fasciolosis is particularly sensitive to human related changes. This zoonosis caused by the parasite Fasciola hepatica, is commonly recognized as a veterinary problem and major public health issue in certain countries. Our study aims to understand the circulation dynamics and risks of fasciolosis emergence in a context of high anthropization. Our objective is (1) to study the dynamics of the intermediate host, a mollusc of the lymnaieidae family. (2) to understand the dynamics and diversity of the parasite between and within its different definitive host compartments. This work was carried out in the Camargue in the Tour du Valat estate, allowing us to have access to the definitive hosts, wild (nutria and wild boars), domestic (treated and untreated bulls) and the intermediate host, Galba truncatula. First, we characterized the habitats that are favorable to the intermediate host G. truncatula, presence in Camargue and we found that ponds appear to be areas of higher risk than irrigation channels for fasciolosis transmission. Then, we became interested in the influence of habitats on the dynamics of G. truncatula through population genetics approaches, our results showed that habitat permanence and connectivity influence the reproduction mode, population structure and dispersal of G. truncatula in the Camargue. In a second step, we studied the dynamics and circulation of the parasite within the definitive host compartment. Our results of the population genetic analyses of definitive hosts indicated that there were several transmission sites on our study area that constituted a single large global outbreak. In addition, the study of the circulation of the parasite between wildlife and domestic animals suggests the role of wild boars in the spread of the disease and the role of nutrias in maintaining the fasciolosis cycle. Our work highlights the value of long term studies and the importance of taking into account all the compartments involved to understand the epidemiology of a disease. They also emphasize the role of human activities and ecosystem in the dynamics of fasciolosis. The ultimate goal of this study is to propose integrated management measures adapted to the Camargue context in order to limit the health impact of fasciolosis and other livestock diseases in the region.