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.

<p>Genetic diversity, population structure, and connectivity influence interactions among communities and populations. At hydrothermal vents in the western pacific, population structure in vent-associated species could occur at spatial scales ranging from vent sites separated by a few hundred meters to oceanic basins separated by more than 3000 kilometers. The spatial scale of population structure has important conservation implications; species that are well-connected across large geographic regions are more resilient to natural and anthropogenic disturbance. This dissertation examines the genetic diversity, population structure, and connectivity of 3 vent-associated species in the western Pacific. It first presents results from the development of microsatellite primers for Ifremeria nautilei, a deep-sea vent associated snail, then uses mitochondrial COI sequences and a suite of microsatellite markers to examine the broader connectivity of three vent-associated species, Ifremeria nautilei, Chorocaris sp. 2, and Olgasolaris tollmanni, across three back-arc basins in the western Pacific. </p><p>Within Manus Basin, no significant genetic differentiation was detected in populations of Ifremeria nautilei (based on COI and microsatellite), Chorocaris sp. 2 (based on COI and microsatellite), or Olgasolaris tollmanni (based on COI). A previously documented low-abundance cryptic species, Chorocaris sp. 1, was detected from a single site, South Su (based on COI). The population of I. nautilei in Manus Basin was found to be significantly differentiated from a second population that appeared to be panmictic across North Fiji and Lau Basin (based on COI and microsatellites). Chorocaris sp. 2 was also found to be significantly differentiated between Manus and North Fiji Basin (based on COI). Both I. nautilei and Chorocaris sp. 2 showed signs of potential low-level migration between Manus and other southwestern Pacific basins. O. tollmanni was undifferentiated between Manus and Lau Basin (based on COI). It is likely that a variable impedance filter exists that limits the realized dispersal of some, but not all species between Manus Basin and other western Pacific back-arc basins. The presence of a variable filter has implications for the conservation and management of hydrothermal vents in Manus Basin, as it is unclear what effects sustained anthropogenic disturbance will have on isolated populations of I. nautilei and Chorocaris sp. 2.</p> / Dissertation

Pollination, one of our ecosystem services, is considered to be in critical condition due to a worldwide reduction in pollinators and their biodiversity. As the agricultural landscape becomes more and more intense, the pollinators lose important food and living resources.     In temperate ecosystems, bumblebees (Bombus spp) are an important group of wild pollinators, and as with pollinators in general, they are declining in both abundance and richness, in Sweden as well as other countries.      The purpose of this study was to see if bumblebee species number of a location is linked to the location’s number of flowering angiosperm species in northwestern Scania when examining eight locations, and to see if gene flow existed between four chosen locations.        The result of this study suggests that it is not possible to tell from the flowering angiosperm species how many bumblebee species that will be abundant, but that it might be possible to tell the number of bumblebee individuals. With the number of bumblebee species, the abundant Fabaceae species was more important than the total number of flowering angiosperms of the location. The number of abundant Fabaceae species was strongly correlated to the bumblebee diversity index of the locations, indicating that it is a group of flowers closely linked to bumblebees.      To see if gene flow occurred between the chosen locations, mtDNA sequences were compared in neighbor joining trees. The result showed that though some tendencies of isolation existed, gene flow seemed to occur in general between the locations in that fragmented and human dominated landscape of northwestern Scania.

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

Habitat connectivity is important to maintain in order to prevent loss of genetic diversity, reduce inbreeding depression, and decrease extinction risk in threatened or endangered species. Here I present a landscape genetics study on marbled salamanders (Ambystoma opacum) in highly connected forested habitat at Mammoth Cave National Park. This investigation of gene flow among ponds within a mostly continuous landscape provides data that can be compared with patterns observed in more fragmented landscapes. These comparisons can provide a means of investigating the separate effects of structural and functional habitat connectivity on amphibian genetic population structure. Structural connectivity refers to the pattern of available habitat, and functional connectivity refers to the organism’s response to the available habitat (i.e., use of alternative habitat types). Five hundred fifty-six individuals were sampled from 50 ponds and screened at eight microsatellite loci to look for genetic population structure. Structure did exist at the park, with the best predictor of breeding pond isolation being interpond distance. Wet deciduous forest appears to offer lower resistance to gene flow in this species than dry deciduous or coniferous forest habitat, while the Green River appears to serve as a partial barrier to gene flow. Overall, my data suggest that marbled salamanders at Mammoth Cave National Park frequently move among breeding ponds, and these individuals within these ponds experience extensive amounts of gene flow. This confirms that the seemingly continuous pattern of habitat at Mammoth Cave National Park has resulted in well-connected subpopulations that frequently share genetic material.

The natural instability of hydrothermal vents creates variable environmental conditions among habitat patches. Habitat differences correspond to phenotypic variation in Ridgeia piscesae, the only ‘vent tubeworm’ on the spreading ridges of the Northeast Pacific. Ridgeia piscesae that occupy high fluid flux habitats have rapid growth rates and high reproductive output compared to tubeworms in habitats with low rates of venting fluid delivery. As recruitment occurs in all settings, worms in the “optimal habitat” may act as source populations for all habitat types. Ridgeia piscesae is a foundation species in the Endeavour Hydrothermal Vents Marine Protected Area of the Juan de Fuca Ridge. The objective of this thesis was to assess fine scale population structure in Ridgeia piscesae within the Endeavour vent system using genetic data. Population structure was assessed by analysis of the mitochondrial COI gene in 498 individuals collected from three vent sites of the Juan de Fuca Ridge; Middle Valley (n=26), Endeavour Segment (n=444) and Axial Volcano (n=28). Genotyping using microsatellite markers was attempted but all loci developed for closely related tubeworm species failed to amplify microsatellites in Ridgeia piscesae. Sequence analysis identified 32 mitochondrial COI haplotypes; one dominant haplotype (68%), three common haplotypes (4%-7%) and the remainder were rare (<2%). Axial Volcano was differentiated from Middle Valley and Endeavour. Within Endeavour, genetic sub-structuring of Ridgeia piscesae occurred among vent fields (Clam Bed, Main Endeavour and Mothra) and habitat types < 10 km apart. Patterns of genetic variation and coalescent based models suggested that gene flow among vent fields moved in a north to south direction in individuals from high flux habitat but from south to north in individuals from low flux habitat. Tubeworms from low flux habitat had more nucleotide polymorphisms and haplotypes than those from high flux habitats. Estimates of the number of immigrants per generation moving from high flux to low flux subpopulations was four times higher than in the reverse direction. The effective population size was estimated to be three times greater in high flux habitat when the generation times for individuals from each habitat type were considered. Demographic tests for population equilibrium identified a recent and rapidly expanding metapopulation at Endeavour. Models of gene flow in Ridgeia piscesae reflected the general oceanographic circulation described at Endeavour. Genetic data illustrate that dispersing larvae exploit the bi-directional currents created through plume driven circulation within the Endeavour axial valley and suggest that adult position on or near chimneys may influence larval dispersal trajectories upon release. Building on known ecological and biological features, this study also showed that Ridgeia piscesae from limited and ephemeral high flux habitat act as sources to the overall metapopulation and that asymmetrical migration and habitat stability sustain high genetic diversity in low flux sinks. The overall metapopulation at Endeavour experiences frequent extinction and recolonization events, differences in individual reproductive success, and source-sink dynamics that decrease the overall effective size and genetic diversity within the population. These factors have important implications for the conservation of a foundation species. / Graduate / 0307 / 0329 / 0369 / lcpuetz@uvic.ca

The theory of "genomic islands of speciation" has been extensively debated during the last decade. This thesis not only supports this theory, but provides evidence that challenges previous beliefs on the level of admixture between species. The recently published Heliconius melpomene genome project reported apparent genomic paraphyly of H. pardalinus with regard to H. elevatus (Heliconius Genome Consortium 2012). Here, we investigate this pair of butterfly species more fully, firstly by using whole-genome resequence data, and secondly by analyzing additional geographic populations of both species, as well as outgroup taxa. Using a nuclear whole-genome phylogenetic analysis we also confirm that H. elevatus is paraphyletic. The genome-wide phylogenetic signal in H. pardalinus and H. elevatus does not indicate expected mutual monophyly of each species as it seems strongly distorted by a high level of admixture. However, several regions of the genome remain differentiated and do show the presumably original phylogenetic signal with mutual monophyly of H. pardalinus and H. elevatus. The genomic background is so homogenized that its level of differentiation (FST ~ 0.03) virtually implies panmixia. The pattern of a high level of homogenization across the genome with several regions of differentiation was consistent with a number of other statistics such as absolute divergence Dxy, nucleotide polymorphism π, number of fixed differences and with a sliding window phylogeny. The identified genomic islands of divergence comprise genes responsible for wing-patterning and chemosensation in Heliconius and some of these genes are found to be under positive selection, suggesting possible candidates of speciation.

Diss. (sammanfattning). Uppsala : Sveriges lantbruksuniversitet, 2004. / Härtill 4 uppsatser.

Thesis (MScAgric)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: See full text for abstract / AFRIKAANSE OPSOMMING: Sien volteks vir opsomming

A erva-mate, Ilex paraguariensis, é uma espécie dioica, clímax com ampla área de distribuição natural. A despeito de sua importância econômica e ecológica são escassos os estudos de conservação e genética da espécie. O objetivo geral do trabalho foi estudar a diversidade genética, a estrutura genética espacial e o fluxo gênico por dispersão de sementes em duas populações naturais de I. paraguariensis na área do entorno do Parque Nacional do Iguaçu, com uso de marcadores moleculares microssatélites. Foram encontrados baixos níveis de diversidade genética em oito loci analisados, com divergência genética maior entre do que dentro das populações. A I. paraguariensis apresentou baixa densidade populacional, com 0,27 a 0,29 árvores por ha-1 e distribuição espacial agregada, entretanto não foi observado evidência de estrutura genética espacial. A média da distância da dispersão de pólen foi de 393 m e a dispersão de sementes atingiu distância próximas a 2.000 m. Os resultados obtidos, sugerem que a base genética da espécie não é ampla, o que pode dispor a I. paraguariensis a um estado crítico de conservação, devido a de erosão genética provocada pela destruição de seus ambientes naturais. / The yerba mate, Ilex paraguariensis, is a species dioecious, climax with wide natural range. Despite their economic and ecological importance are few studies of genetics and conservation of the specie. The overall objective this work was to study the genetic diversity, spatial genetic structure and gene flow by seed dispersal in two natural populations of I. paraguariensis around the National Park of Iguassu, using microsatellite molecular markers. It found low levels of genetic diversity at eight loci analyzed, and greater genetic divergence between populations than within population. The I. paraguariensis showed low population density with 0.27 to 0.29 trees per ha-1 and spatial clustered distribution, however was not observed evidence of spatial genetic structure. The average distance of pollen dispersal was 393 m and seed dispersal reached near 2,000 m. The results suggest that the genetic basis of species is not large, which may carry the I. paraguariensis to critical state of conservation due to genetic erosion caused by the destruction of their natural environments.