Neogene land-mammal localities are very rare in the northeastern U.S.; therefore, the late Miocene/early Pliocene Gray Fossil Site in eastern Tennessee can clarify paleoecological dynamics during a time of dramatic global change. In particular, the identification of ancient forests and past climate regimes will better our understanding of the environmental context of mammalian evolution during the late Cenozoic. Stable isotope analyses of bulk and serial samples of fossil tooth enamel from all ungulates present at the Gray site elucidate paleoecological reconstructions. The herbivorous megafauna include taxa of likely North American and Eurasian ancestry including: the tapir Tapirus polkensis, rhino Teleoceras cf. T. hicksi, camel cf. Megatylopus sp., peccary Tayassuidae, and proboscidean Gomphotheriidae. The tapir, rhino, camel, and peccary yield mean stable carbon isotope (δ13C) tooth enamel values of - 13.0‰, - 13.3‰, - 13.8‰, and - 13.1‰, respectively, suggesting forest-dwelling browsers. This range of δ13C values indicates the presence of a C3 dominated ancient local flora. Because δ13C values decline with increasing canopy density, the ancient temperate forests from the Gray site were moderately dense. The lack of significant C4 plant consumption (i.e., tooth enamel δ13C values < - 9‰) suggests the presence of forests large enough to independently support the continued browsing of sustainable populations of browsers from the Gray site. In contrast, bulk and serial δ13C values ranging from - 0.7‰ to 0.3‰ from a gomphothere tusk support a diet consisting of C4 grasses, suggesting the presence of C4 grasslands within the individuals home range. The rare earth element (REE) analyses of the gomphothere tusk and the teeth of Tapirus and Teleoceras indicates that these individuals shared similar depositional environments; thus, demonstrating the concurrent presence of C3 forests and C4 grasslands in the northeast. Stable carbon and oxygen serial sample variation of the tapir, rhino, peccary, and gomphothere is less than 1.5‰, suggesting minor differences in seasonal temperature and/or precipitation. These data support the possibility of a North American forest refugium in the southern Appalachians during a time typified by more open environments.

Climate change is one of the most important factor determining species ranges. In Europe there is now evidence for northward areal expansion in many Mediterranean insects including the praying mantis (Mantis religiosa). This species is the only representative of the order Mantodea inhabiting central Europe. The northern edge of the species distribution currently reaches latitude 53ř North. Although, the praying mantis is well known insect there is not enough evidence about its phylogeography. In this work three mitochondrial genes (COI, COII, Cyt b) were selected for phylogenetic study. Results indicate three statistically supported distinct lineages in Europe: Eastern European, Central European and Western European. Presumably these lineages are consistent with isolation during the last glacial and re-colonization from glacial refugia. Reduced haplotype diversity on the northern edge suggests currently established populations at the northern distribution border. To validate mtDNA results it was also considered four microsatellite loci. Due to different type of inheritance mtDNA and nuclear DNA it is possible to compare two independent genetic datasets. Microsatellite analysis confirmed results obtained on mitochondrial data. Three major genetic clusters were found: east, west and central. Spatial...

A multidisciplinary research methodology based on the combination of literature review and spatial analysis is presented as a contribution to the historical ecology of olive trees in Sicily (Italy). The thesis crosscuts time and space at different scales for a new epistemological approach to allow the olive trees to “talk”. Structured around the identification of breaking points and nodes of connection, the social and ecological history of the olive trees in the island are explored. While recognising the full agency of trees in the spatial and temporal evolving dynamics of the landscape, the vital importance of their inner connections with other elements of the ecosystems is stressed in the analysis; as also the importance of Traditional Ecological Knowledge. The thesis is concluded with the hypothesis that the olive trees of Sicily could be seen as biocultural refugia, physical places which preserve both agricultural biodiversity and traditional ecological knowledge.

O contato pretérito Amazônia-Mata Atlântica vem sendo recorrentemente citado na literatura para diversos grupos da fauna Neotropical e teria ocorrido por diferentes rotas geográficas e períodos temporais. Segundo esta hipótese, em períodos quentes e úmidos as florestas se expandiram provocando retração/fragmentação das áreas abertas, ao passo que em períodos frios e secos, o inverso ocorreria. Assim, utilizando-se de crotalíneos como modelo, esta tese pretende: (1) testar o pretérito contato Amazônia-Mata Atlântica, assim como o tempo de separação entre as linhagens relictuais nesses ambientes florestados, elucidando a história demográfica das espécies de Bothrops do grupo jararacuçu, do grupo atrox e de B. bilineatus; (2) paralelamente Crotalus durissus, espécie associada à diagonal de áreas abertas da América do Sul (Caatinga, Cerrado e Chaco), foi utilizada para testar a ocorrência de expansão desses ambientes, o que levaria a quebra da hipotetizada ponte florestada Amazônia-Mata Atlântica. Através de dataset multi-locus sob Inferência Bayesiana (quatro genes mitocondriais e cinco nucleares) foram testadas as relações filogenéticas e filogeográficas entre as amostras em Bothrops e Crotalus. Cenários históricos alternativos foram testados com base em simulações coalescentes e ABC (approximate Bayesian computation). Adicionalmente, foi empregado teste de delimitação de linhagens evolutivas para o reconhecimento da diversidade, a nível de espécie, em cada grupo estudado, usando a implementação Bayesiana do algoritimo Generalized Mixed Yule-Coalescent. Os resultados filogenéticos e análises de delimitação de espécies indicam diversidade críptica para os grupos jararacussu, atrox e taeniatus. Os testes de cenários históricos sugerem (1) múltiplas conexões florestais Amazônia-Mata Atlântica nos últimos 2.5 milhões de anos, com intercâmbio faunístico em ambas as direções e (2) expansão das áreas abertas do Cerrado e Caatinga em sincronia temporal com perda de conectividade florestal Amazônia-Mata Atlântica durante o Pleistoceno tardio (3) que a formação e estabilização do Rio Amazonas teve influência na diversificação do grupo jararacuçu, gerando diversidade. Os resultados trazem informações sobre o dinamismo histórico das paisagens florestadas e abertas no Neotrópico ao longo do tempo, assim como o papel dos rios amazônicos na diversificação da fauna. Adicionalmente, os resultados apontam para instabilidade taxonômica e diversidade críptica em diversos grupos em Bothrops e em Crotalus durissus, revelando a necessidade do aprofundamento sistemático para essas serpentes venenosas de importância médica / The hypotetized historical contact Amazon-Atlantic Forest has been recurrently cited in the literature for several groups of Neotropical fauna and would have occurred by different geographic routes and time periods. According to this hypothesis, in hot and humid periods the forests expanded causing retraction / fragmentation of the open areas, while in cold and dry periods, the reverse would occur. Thus, by using Neotropical pit vipers as a model, this thesis aims to: (1) test the historical forest contact Amazon-Atlantic Forest, as well as the time of separation between relict lineages in these forested environments, elucidating the demographic history of Bothrops species from jararacussu group, atrox group and B. bilineatus; (2) Crotalus durissus, a species associated with the diagonal of open areas of South America (Caatinga, Cerrado and Chaco), was used in parallel to test the occurrence of expansion of these environments, which would lead to the breakage of the hypothetical Amazon-Atlantic Forest forested bridge. Phylogenetic and phylogeographic relationships between samples of Bothrops and Crotalus were tested through a multi-locus dataset (four mitochondrial genes and five nuclear) under Bayesian Inference. Alternative historical scenarios were tested based on coalescent simulations and ABC (approximate Bayesian computation). In addition, was inferred independently evolving lineages to recognized species diversity in each group studied, using Bayesian implementation of the molecular species delimitation algorithm Generalized Mixed Yule-Coalescent. Phylogenetic results and analyzes of species delimitation indicate cryptic diversity for the groups jararacussu, atrox and taeniatus. The tests of historical scenarios suggest (1) multiple Amazon-Atlantic Forest forest connections in the last 2.5 million years, with faunal exchange in both directions and (2) expansion of the open areas of the Cerrado and Caatinga in temporal synchrony with loss of forest bridge Amazon-Atlantic Forest during late Pleistocene (3) that the formation and stabilization of the Amazon River influenced the diversification of the jararacussu group, generating diversity. The results provide information on the historical dynamism of forested and open landscapes in the Neotropics over time, as well as the role of Amazonian rivers in the diversification of fauna. Moreover, the results point to taxonomic instability and cryptic diversity in several groups within Brothrops and Crotalus durissus, revealing the need for systematic deepening for these medically important venemous snakes

Quaking aspen (Populus tremuloides) has the largest natural distribution of any tree native to North America, ranging from Alaska through the breadth of Canada and south to mid-Mexico. The Laurentide ice sheet occupied most of the current range of P. tremuloides until the late Pleistocene epoch, so this species has undergone a significant, geologically recent range expansion. Surprisingly, range-wide patterns of genetic variation in P. tremuloides have never been described. Using a sample set representing the full longitudinal and latitudinal extent of the species distribution, I have conducted a phylogeographic analysis for P. tremuloides. Preliminary results comparing both nuclear and chloroplast DNA sequences revealed surprisingly low levels of divergence across the range. Because of this remarkably shallow genetic divergence among aspen populations, I used a set of rapidly-evolving molecular markers (microsatellites) to describe patterns of gene flow and diversity and to correlate those patterns with landscape features and histories. I analyzed eight microsatellite loci in 794 individuals from 30 sampling sites. From this multilocus data set, I identified pronounced genetic structuring across the range. Strikingly, sampling sites representing the southwestern portion of the range, the western United States and Mexico, form a distinct cluster. Sites within this southwestern cluster display dramatically reduced within-site genetic diversity but elevated regional genetic diversity, which suggests that populations in the southwestern portion of the range make up a stable edge persisting through multiple climate oscillations. Based on the uniqueness of the southwestern cluster and the climatic differences between the southwest and northern portions of the range, I propose that the southwestern cluster may represent a distinct ecotype. I also identified hotspots of diversity that correspond with potential refugia during the last glacial maximum but additional work is needed to refine these patterns. Further, my findings provide a solid foundation for a range of future studies on adaptive genetic and trait variation in this species.

<p>The aim of this thesis is to study phylogeny, species-wide phylogeography and genetic diversity in <i>Formica</i> ants across Eurasia in connection with the history of biotic responses to Quaternary environmental changes.</p><p>The mitochondrial DNA phylogeny of Palaearctic <i>Formica</i> species supported the subgeneric grouping based on morphological similarity. The exception was that <i>F. uralensis</i> formed a separate phylogenetic group. The mitochondrial DNA phylogeny of the <i>F. rufa </i>group showed the division into three major phylogenetic groups: one with the species <i>F. polyctena</i> and <i>F. rufa</i>, one with <i>F. aquilonia</i>, <i>F. lugubris</i> and <i>F. paralugubris</i>, and the third one with <i>F. pratensis</i>.</p><p>West-east phylogeographic divisions were found in <i>F. pratensis</i> suggesting post-glacial colonization of western Europe and a wide area from Sweden to the Baikal Lake from separate forest refugia. In contrast, no phylogeographic divisions were detected in either <i>F. lugubris </i>or<i> F. exsecta</i>. Contraction of the distribution range to a single refugial area during the late Pleistocene and the following population expansion could offer a general explanation for the lack of phylogeographic structure across most of Eurasia in these species.</p><p>Sympatrically distributed and ecologically similar species <i>F. uralensis </i>and<i> F. candida</i> showed clear difference in the phylogeographic structure that reflected difference in their vicariant history. Whereas no phylogeographic divisions were detected in <i>F. uralensis</i> across Europe, <i>F. candida</i> showed a well-supported phylogeographic division between the western, the central and the southern group.</p><p>In socially polymorphic <i>F. cinerea</i>, the overall level of intrapopulation microsatellite diversity was relatively high and differentiation among populations was low, indicating recent historical connections. The lack of correspondence between genetic affinities and geographic locations of studied populations did not provide any evidence for differentiating between alternative hypotheses concerning the directions and sources of postglacial colonization of Fennoscandia.</p>

Anthropogenic influences and climate change are warming rivers in New Brunswick and threatening the cold water habitats of native salmonids. When ambient river temperatures in summer exceed the tolerance level of Atlantic salmon and brook trout, individuals behaviourally thermoregulate by seeking out cold water refugia. These critical thermal habitats are often created by tributaries and concentrated groundwater discharge. Thermal infrared imagery was used to map cold water anomalies along a 53 km reach of the Cains River on 23 July 2008. Although efficient and useful for mapping surface temperature of a continuous stream reach, the fish did not use all identified thermal anomalies as refugia. Overall, 100 % of observed large brook trout >35 cm in length were found in 30 % of the TIR-mapped cold water anomalies. Ninety eight percent of observed small brook trout 8 – 30 cm in length were found in 80 % of the mapped cold water anomalies and their densities within anomalies were significantly higher than densities outside of anomalies. Fifty nine percent of observed salmon parr were found in 65 % of the mapped anomalies; however, they were dispersed within study sites and their densities were not significantly different within anomalies compared to outside of the anomalies. No brook trout were observed at the seven noncold water study sites that were investigated. Preference curves for various habitat variables including velocity, temperature, depth, substrate, and deep water availability near cold water anomalies were developed based on field investigations during high temperature events (ambient river temperature >21 oC). Combined with thermal imagery, managers can use the physical descriptions of thermal refugia developed here as a tool to help conserve and restore critical thermal refugia for Atlantic salmon and brook trout on the Cains River, and potentially similar river systems.

The aim of this thesis is to study phylogeny, species-wide phylogeography and genetic diversity in Formica ants across Eurasia in connection with the history of biotic responses to Quaternary environmental changes. The mitochondrial DNA phylogeny of Palaearctic Formica species supported the subgeneric grouping based on morphological similarity. The exception was that F. uralensis formed a separate phylogenetic group. The mitochondrial DNA phylogeny of the F. rufa group showed the division into three major phylogenetic groups: one with the species F. polyctena and F. rufa, one with F. aquilonia, F. lugubris and F. paralugubris, and the third one with F. pratensis. West-east phylogeographic divisions were found in F. pratensis suggesting post-glacial colonization of western Europe and a wide area from Sweden to the Baikal Lake from separate forest refugia. In contrast, no phylogeographic divisions were detected in either F. lugubris or F. exsecta. Contraction of the distribution range to a single refugial area during the late Pleistocene and the following population expansion could offer a general explanation for the lack of phylogeographic structure across most of Eurasia in these species. Sympatrically distributed and ecologically similar species F. uralensis and F. candida showed clear difference in the phylogeographic structure that reflected difference in their vicariant history. Whereas no phylogeographic divisions were detected in F. uralensis across Europe, F. candida showed a well-supported phylogeographic division between the western, the central and the southern group. In socially polymorphic F. cinerea, the overall level of intrapopulation microsatellite diversity was relatively high and differentiation among populations was low, indicating recent historical connections. The lack of correspondence between genetic affinities and geographic locations of studied populations did not provide any evidence for differentiating between alternative hypotheses concerning the directions and sources of postglacial colonization of Fennoscandia.

This study examined modifications made by Pogonomyrmex barbatus, by their processes of granivory and nest construction, to forb and grass dynamics under large-scale disturbances of fire, recent drought and long-term, large-mammalian herbivory using comparative studies, field experimental manipulations, and a simulation model on the Edwards Plateau, Texas. Ant nests are refugia for grass survival during extreme droughts as demonstrated during the drought of 1998 to 2002. Significantly greater cover of grasses and lower abundance and cover of forbs was found beside nests compared with surrounding habitat throughout the drought and recovery. Grasses near nests may be the seed source for surrounding habitats during recovery. Seeds were differentially collected among most forbs and grasses despite seed abundance. Harvest was significantly reduced in the fall relative to spring. During preference experiments, harvest differences were found between grazing treatments for two of four species, but only during the spring. High lipid content seeds were unpreferred in fall compared to high protein and carbohydrate content seeds. Granivory influences on seedling establishment were studied by comparing seedling recruitment among sown and naturally occurring seeds excluded and open to foragers. Exclosures were placed in three nest densities and two burn treatments. Seeds in exclosures produced significantly more seedlings than open arenas only during the first year of drought recovery. Densities of grasses and annual forbs were higher in open arenas the second year due to indirect effects of granivory. By reducing seeds ants release seedlings from competition. Sown seedling abundance was unaffected by colony density and fire. Colony density and distribution were influenced by topography, soil types, soil depth and woody cover, but not by historical grazing treatments. Cleared vegetation on nest disks impacted less than 1% of total surface area and losses were compensated by greater basal cover of grasses next to disks compared to surrounding habitats. Foraging areas influenced 17.3-73.6% of surface area and could diminish seed populations for potential seedlings. Model results agree with experimental observations that communities may be modified by P. barbatus presence due to differential responses of grass species to interaction between nests or granivory and rainfall amounts.

Thesis (M.A.P.S.)--Catholic Theological Union at Chicago, 2001. / Vita. Includes bibliographical references (leaves [66]-67).