Submitted by Claudia Rocha (claudia.rocha@udesc.br) on 2017-12-08T13:26:49Z No. of bitstreams: 1 PGEF16MA065.pdf: 6035776 bytes, checksum: 25dd564cad038604abbda9d8984a650c (MD5) / Made available in DSpace on 2017-12-08T13:26:49Z (GMT). No. of bitstreams: 1 PGEF16MA065.pdf: 6035776 bytes, checksum: 25dd564cad038604abbda9d8984a650c (MD5) Previous issue date: 2016-07-14 / FAPESC / The xylem study of arboreal species allows us to identify anatomical characters that show changes in growth and development of individuals. Whereas the plant organization levels are highly integrated and harmonized with the physical environment, this paper aimed to (i) - featuring anatomically (quantitative and qualitative) the wood six species in three Araucaria Forest fragments; (ii) - study the intraspecific relationships of anatomical characters of the species; (iii) - to study the interspecific relationships of anatomical characters and regional climate variables. The samples were collect in Araucaria Forest fragments, in the state of Santa Catarina in the municipalities of Otacílio Costa (840 m), Painel (1340 m) and Urubici (1603 m) with increment borer. Anatomical cuts were obtain in a microtome slide, in anatomical planes: transverse, tangential and radial. Sections were stained with 0.8% safranin, thus dehydrated in ascending alcohol series and fixed in butyl acetate, for mounting the permanent histological blade with Entellan® adhesive. Dissociated elements of wood were also analyzed, it was stained with safranin 0.8%, and mounted on histological blade. Quantitative characteristics were measure in LAS Interactive Measurements software and qualitative, described as the IAWA Committee's recommendations. For quantitative data, the minimum, average and maximum values were presente. The normality of anatomical variables was verified by the Shapiro-Wilk test. Data from the intraspecific analysis were compared using analysis of variance or Kruskal-Wallis test for non-normal distributions, after by Tukey HSD test or test for multiple comparisons non-parametric. To study the relationship between the anatomical characteristics of the wood and the regional climate used a multivariate approach with the combination of RLQ analysis and the fourth corner method by R program along with the vegan libraries, usdm and raster and RFC. The vessel member length, vessel diameter and frequency were the anatomical features that showed more altitudinal gradient influences. The condition of nebular forest, revealed the occurrence of a pattern of ecological strategy associated to water efficiency / O estudo do xilema de espécies arbóreas permite identificar caracteres anatômicos que podem evidenciar possíveis variações no crescimento e no desenvolvimento dos indivíduos. Considerando que os níveis de organização das plantas são altamente integrados e harmonizados com o ambiente físico, o presente trabalho teve como objetivos (i) - caracterizar anatomicamente (quantitativa e qualitativa) o lenho de seis espécies arbóreas em três fragmentos de Floresta Ombrófila Mista; (ii) - estudar as relações intraespecífica dos caracteres anatômicos das espécies; (iii) - estudar as relações interespecífica dos caráteres anatômicos e das variáveis climáticas regionais. As amostras foram coletadas em fragmentos de Floresta Ombrófila Mista, no Estado de Santa Catarina, nos Municípios de Otacílio Costa (840 m), Painel (1340 m) e Urubici (1603 m) com o auxílio de trado de incremento. Foram confeccionados cortes em micrótomo de deslize, nos planos anatômicos: transversal, tangencial e radial. Os cortes foram tingidos com safranina, desidratados em série alcoólica ascendente e fixados em acetato de butila, para a montagem das lâminas permanentes com auxílio de Entellan®. Também foram analisados os elementos dissociados, sendo corado com safranina e montado em lâminas semipermanentes. As características quantitativas foram mensuradas em software Software LAS Interactive Measurements e as qualitativas descritas conforme às recomendações do IAWA Committee para o lenho. Para os dados quantitativos, foram apresentados os valores mínimo, médio e máximo. A normalidade das variáveis anatômicas foi verificada por meio do teste de Shapiro-Wilk. Os dados da análise intraespecífica foram comparados por meio de Análise de Variância (ANOVA) ou pelo teste de Kruskal-Wallis, para distribuições não normais, seguidas pelo teste de Tukey HSD ou pelo teste de comparações múltiplas não-paramétrico. Para o estudo das relações entre os atributos anatômicos da madeira das espécies e o clima regional utilizou-se uma abordagem multivariada com a combinação da análise RLQ e o método “fourth corner” por meio do programa R junto com as bibliotecas vegan, usdm e a raster e RFc. O comprimento, o diâmetro e a frequência dos vasos foram as características anatômicas que mais apresentaram influências do gradiente de altitude. A condição de floresta nebular, revelou a ocorrência de um padrão de estratégia ecológica relacionado a eficiência hídrica

Many previous studies in evolutionary genetics have been based on few model organisms that can be reared at ease in the laboratory. In contrast, genetic studies of non-model, natural populations are desirable as they provide a wider range of adaptive phenotypes throughout evolutionary timescales and allow a more realistic understanding of how natural selection drives adaptive evolution. This thesis represents an example of how modern genomic tools can be effectively used to study adaptation in natural populations. Atlantic herring is one of the world’s most numerous fish having multiple populations with phenotypic differences adapted to strikingly different environments. Our study demonstrated insignificant level of genetic drift in herring that resulted in minute genetic differences in the majority of the genome among these populations. In contrast, a small percentage of the loci showed striking genetic differentiation that were potentially under natural selection. We identified loci associated with adaptation to the Baltic Sea and with seasonal reproduction (spring- and autumn-spawning) and demonstrated that ecological adaptation in Atlantic herring is highly polygenic but controlled by a finite number of loci. The study of Darwin’s finches constitutes a breakthrough in characterizing their evolution. We identified two loci, ALX1 and HMGA2, which most likely are the two most prominent loci that contributed to beak diversification and thereby to expanded food utilization. These loci have played a key role in adaptive evolution of Darwin’s finches. Our study also demonstrated that interspecies gene flow played a significant role in the radiation of Darwin’s finches and some species have a mixed ancestry. This thesis also explored the genetic basis for the remarkable phenotypic differences between three male morphs in the ruff. Identification of two different versions of a 4.5 MB inversion in Satellites and Faeders that occurred about 4 million years ago revealed clues about the genetic foundation of male mating strategies in ruff. We highlighted two genes in the inverted region; HSD17B2 that affects metabolism of testosterone and MC1R that has a key role in regulating pigmentation, as the major loci associated with this adaptation.

The eastern tropical north Pacific (ETNP) is characterized by one of the ocean's most severe midwater oxygen minimum zones (OMZs), where oxygen levels are often less than 5 µM. The copepod family Eucalanidae is a numerically abundant and diverse zooplankton group in the ETNP, and displays a wide range of vertical distributions related to environmental oxygen concentrations. The goal of this dissertation was to develop a better understanding of the ecology, physiology, and biochemistry of closely related copepod species (family Eucalanidae) that inhabit the ETNP OMZ system. This was accomplished through examining different parameters relating to (1) metabolic rates, (2) detailed lipid composition and biomarkers, and (3) body composition, enzyme activity and survivorship in low oxygen water. Oxygen consumption, ammonium, urea, and phosphate excretion rates were generally highest in Subeucalanus subtenuis, a copepod primarily residing in the upper euphotic zone. Eucalanus inermis, typically found in the lowest oxygen environment of the species examined, showed significantly lower metabolic rates largely due to high water content. Rhincalanus rostrifrons, residing primarily in the upper oxycline, showed intermediate rates, likely relating to its higher reliance on lipid catabolism than S. subtenuis and E. inermis. Urea excretion rates showed a complicated relationship with temperature and oxygen, which calls for further study. Knowledge of such interactions is necessary for accurate modeling of nitrogen cycles in OMZ and other oceanic regions. Lipid biomarkers suggested that S. subtenuis, E. inermis and Pareucalanus attenuatus all fed primarily on particulates near the chlorophyll maximum region, while R. rostrifrons and R. nasutus likely fed on sinking particulates at depth. These results also emphasized the difference in lipid composition between wax esters and triacylglycerol components of storage lipids. This study suggested a much larger role of phylogeny in characterizing lipid contents than previously thought. Body composition, enzyme assays and survivorship studies suggested that E. inermis, S. subtenuis, P. attenuatus, R. nasutus and R. rostrifrons formed four separate ecological groups based on genus. E. inermis had low organic matter, moderate lactate dehydrogenase (LDH) activity, and high survivorship at oxygen concentrations < 20 µM. Rhincalanus spp. also had moderate LDH activity and high survivorship in low oxygen, but were unique in particularly low protein and high lipid content. S. subtenuis was characterized by high protein content, no measurable LDH activity and low survivorship in < 20 µM O2. P. attenuatus was similar to S. subtenuis in many respects, but had lower protein content and a different lipid accumulation strategy. In conclusion, eucalanoid copepods utilized many different ecological strategies in the ETNP OMZ system. Features of different ecological groups fit well with their observed vertical distributions in the water column. Understanding the ecology of organisms in OMZ systems will allow us better predictive capability for the effects of expanding OMZs in other regions.

<p dir="ltr">Coastal ecosystems are critically important habitats for the services they provide on a global and local scale. Maritime forests are found within the southern Atlantic coast, and they serve as a boundary between the ocean and land. These forests stabilize coastlines, recharge groundwater, and provide a protective buffer against storm damage. Southern live oak (<i>Quercus virginiana</i>) was historically the dominant canopy species in maritime forests; however, previous land conversions to loblolly pine (<i>Pinus taeda</i>) plantations have shifted the abundance of loblolly pine to become the dominant canopy tree in maritime forests. Loblolly pines are fast growing, and they regenerate vigorously but they are not well adapted to coastal stressor. In recent decades, outbreaks of southern pine beetle (<i>Dendroctonus frontalis</i>) have provided restoration practitioners an opportunity to clear tracts of pine dominated maritime forest to restore live oak to the canopy. This research project is comprised of two experiments studying the performance of planted <i>Q. virginiana</i> seedlings on maritime forest restoration sites in coastal Georgia. The first experiment evaluated planting density (1-meter, 2-meters, 3-meters), mulch (with or without), and fertilizer (with or without). Overall seedling survival was 99% after four years. The application of fertilizer had an initial positive effect on seedling diameter after the first growing season. The application of mulch increased seedling height in the second to fourth growing seasons, diameter in third and fourth, and crown width in the fourth growing season. Planting density had no consistent effect over the first four years, and no biological significance was observed for foliar nutrient content. The second experiment examined eight different groupings of intra- and interspecific competition between <i>Q. virginiana</i> and <i>P. taeda</i> including: oak or pine alone; oak surrounded by oak, pine, or oak/pine; pine surrounded by pine, oak, or pine/oak at 0.5-m spacing between all seedlings. Two years after outplanting, survival did not vary by treatment. Oak centered competition plots were positively impacted by border tree height and diameter in year one and border height positively affected the center tree height in year two. Pine centered competition plots were positively impacted by border tree height in year one and year two. Oak centered competition plots with a mix of oak and pine on the border had significantly lower osmotic potential than other pine centric treatments after two years. Overall, oak centered treatments had lower osmotic potential than pine centered treatments. Ectomycorrhizal (EMF) species composition changed, and relative abundance increased from the initial planting to two years later but there was no variation between treatments and most EMF species were generalists. These results highlight the importance of mulch and fertilizer to reduce transplant shock and how competing seedlings can train seedlings to allocate photosynthate to shoot growth to help promote aboveground growth.</p>

Studying genetic diversity in natural and domestic populations is of major importance in evolutionary biology. The recent advent of next generation sequencing (NGS) technologies has dramatically changed the scope of these studies, enabling researchers to study genetic diversity in a whole-genome context. This thesis details examples of studies using NGS data to: (i) characterize evolutionary forces shaping the genome of the Atlantic herring, (ii) detect the genetic basis of speciation and domestication in the rabbit, and, (iii) identify mutations associated with skeletal atavism in Shetland ponies. The Atlantic herring (Clupea harengus) is the most abundant teleost species inhabiting the North Atlantic. Herring has seasonal reproduction and is adapted to a wide range of salinity (3-35‰) throughout the Baltic Sea and Atlantic Ocean. By using NGS data and whole-genome screening of 20 populations, we revealed the underlying genetic architecture for both adaptive features. Our results demonstrated that differentiated genomic regions have evolved by natural selection and genetic drift has played a subordinate role. The European rabbit (Oryctolagus cuniculus) is native to the Iberian Peninsula, where two rabbit subspecies with partial reproductive isolation have evolved. We performed whole genome sequencing to characterize regions of reduced introgression. Our results suggest key role of gene regulation in triggering genetic incompatibilities in the early stages of reproductive isolation. Moreover, we studied gene expression in testis and found misregulation of many genes in backcross progenies that often show impaired male fertility. We also scanned whole genome of wild and domestic populations and identified differentiated regions that were enriched for non-coding conserved elements. Our results indicated that selection has acted on standing genetic variation, particularly targeting genes expressed in the central nervous system. This finding is consistent with the tame behavior present in domestic rabbits, which allows them to survive and reproduce under the stressful non-natural rearing conditions provided by humans. In Shetland ponies, abnormally developed ulnae and fibulae characterize a skeletal deformity known as skeletal atavism. To explore the genetic basis of this disease, we scanned the genome using whole genome resequencing data. We identified two partially overlapping large deletions in the pseudoautosomal region (PAR) of the sex chromosomes that remove the entire coding sequence of the SHOX gene and part of CRLF2 gene. Based on this finding, we developed a diagnostic test that can be used as a tool to eradicate this inherited disease in horses.

<p dir="ltr">Global forest ecosystems provide essential ecosystem services that contribute to water and climate regulation, food production, recreation, and raw materials. They also serve as crucial habitats for numerous terrestrial species of amphibians, birds, and mammals worldwide. However, recent decades have witnessed unprecedented changes in forest ecosystems due to climate change, shifts in species distribution patterns, increased planted forest areas, and various disturbances such as forest fires, insect infestations, and urbanization. These changes can have far-reaching impacts on ecological networks, human well-being, and the well-being of global forest ecosystems. To address these challenges, I present four studies to quantify forest dynamics through mapping, classification, and projection, using artificial intelligence tools in combination with a vast amount of training data. (I) I present a spatially continuous map of planted forest distribution across East Asia, produced by integrating multiple sources of planted and natural forest data. I found that China contributed 87% of the total planted forest areas in East Asia, most of which are located in the lowland tropical/subtropical regions and Sichuan Basin. I also estimated the dominant genus in each planted forest location. (II) I used continent-wide forest inventory data to compare the range shifts of forest types and their constituent tree species in North America in the past 50 years. I found that forest types shifted more than three times as fast as the average of their constituent tree species. This marked difference was attributable to a predominant positive covariance between tree species ranges and the change of species relative abundance. (III) Based on individual-level field surveys of trees and breeding birds across North America, I characterized New World wood-warbler (<i>Parulidae</i>) species richness and its potential drivers. I identified forest type as the most powerful predictor of New World wood-warbler species richness, which adds valuable evidence to the ongoing physiognomy versus composition debate among ornithologists. (IV) In the appendix, I utilized continent-wide forest inventory data from North America and South America and the combination of supervised and unsupervised machine learning algorithms to produce the first data-driven map of forest types in the Americas. I revealed the distribution of forest types, which are useful for cost-effective forest and biodiversity management and planning. Taken together, these studies provide insight into the dynamics of forest ecosystems at a large geographic scale and have implications for effective decision-making in conservation, management, and global restoration programs in the midst of ongoing global change.</p>