Made available in DSpace on 2014-07-29T16:21:20Z (GMT). No. of bitstreams: 1 Dissertacao Advaldo Ecologia.pdf: 1653523 bytes, checksum: f1b37fbab550f36d115f06121fc017e2 (MD5) Previous issue date: 2012-03-12 / The genus Caryocar is formed by tree species and is distributed in the neotropical region. Many species of the genus are found in forested biomes, but three species are found in the dry diagonal that cuts the two Brazilian biomes of tropical forests: C. brasiliense, C. coriaceum and C. cuneatum. Understand the phylogeographic pattern of these species may help to comprehend the historic events responsible for the actual biogeographic patterns of the region. In this context, the aim of our study was evaluate the genetic variability of the species that are found in the Brazilian dry diagonal, observe how it s distributed in the sampled populations and, from the data, try to construct a phylogeographic hypothesis for the origin of these species. We sequenced two chloroplastic regions, trnH-psbA and trnC-ycf6, from nine species of the genus Caryocar, for a better understanding of the dry diagonal group origin relative to the species that are found in the tropical forests biomes. We inferred the genetic diversity indices; the relationship between the species, using a network and a Bayesian phylogenetic tree; and we inferred the Time to the Most Recent Common Ancestor of the groups of interest using coalescence based methods. We analyzed 785 base pairs and found 23 haplotypes, some of them are shared between species, demonstrating the possibility of incomplete lineage sorting or hybridization between species of the genus. The species presented low genetic diversity indices, and we found genetic structure in the Caryocar brasiliense populations. The populations from the northern and western threshold of the C. brasiliense distribution presented evidences that they may have functioned as a source of migrants to the other populations. The date of the divergence time reveals that the dry diagonal group has originated around 2,48 millions years before present, and the ancestor of the C. coriaceum e C. cuneatum appeared around 1,21 million years before present, at the beginning of the glacial periods, at Pleistocene. It suggests that these glacial periods had influenced the actual distribution of the species. / O gênero Caryocar é composto por espécies arbóreas, distribuído na região neotropical. A maioria das espécies do gênero ocupa biomas florestais, porém três espécies se distribuem na diagonal seca que corta os dois biomas de floresta tropical brasileira sendo elas C. brasiliense, C. coriaceum e C. cuneatum. Entender o padrão filogeográfico dessas espécies pode ajudar na compreensão de eventos históricos responsáveis pelos padrões biogeográficos atuais da região. Nesse contexto, o objetivo de nosso estudo foi avaliar a variabilidade genética existente nas espécies que ocupam a diagonal seca brasileira, observar como ela se encontra distribuída nas populações amostradas e a partir dos dados tentar construir uma hipótese filogeográfica para a origem dessas espécies. Foram sequenciadas duas regiões do genoma cloroplastidial, trnH-psbA e trnC-ycf6, de nove espécies do gênero Caryocar, para a melhor compreensão da origem do grupo da diagonal seca em relação às espécies que ocupam biomas de florestas tropicais. Foram inferidos os índices de diversidade genética; a relação de parentesco entre as espécies por meio de uma rede de haplótipos e de uma árvore filogenética Bayesiana; a estrutura genética das populações; mudanças demográficas históricas; e por fim, o cálculo dos tempos de divergência do grupo em interesse foi realizado por meio da metodologia baseada na teoria de coalescência. Foram analisados 785 pares de base e foram encontrados 23 haplótipos, alguns deles compartilhados entre espécies, demonstrando a possibilidade de retenção de polimorfismo ancestral ou hibridização entre as espécies do gênero. As espécies apresentaram baixos índices de diversidade genética, e foi encontrada estruturação dessa variabilidade na espécie C. brasiliense (ΦST = 0,363). No geral, não houve evidências de grandes mudanças demográficas históricas nas espécies em estudo. As populações do limite norte e oeste da distribuição de C. brasiliense apresentaram evidências de que podem ter funcionado como fonte de migrantes para as demais populações. A datação dos períodos de divergência revelou que o grupo da diagonal seca se originou por volta de 2,48 milhões de anos (Ma) atrás, e o ancestral das espécies C. cuneatum e C. coriaceum surgiu por volta de 1,21 Ma, sugerindo um possível efeito das glaciações pleistocênicas na distribuição atual das espécies.

Anadenanthera é um gênero botânico pertencente à família Mimosaceae e endêmico da América Latina e Caribe. Compreende duas espécies arbóreas tropicais: Anadenanthera colubrina (Vell.) Brenan. (angico, angico vermelho, angico branco, curupay) e Anadenanthera peregrina (L.) Speg. (angico, angico preto, angico de casca, angico do cerrado, yopo ou cohoba). As duas espécies são de ocorrência frequente na paisagem da região de Ribeirão Preto, apresentando-se em aglomerados quase monoespecíficos popularmente conhecidos como angicais. Visando contribuir para futuras medidas conservacionistas, o objetivo deste trabalho foi investigar a diversidade genética, o sistema de reprodução, a estrutura genética espacial e o fluxo gênico contemporâneo de A. colubrina e A. peregrina em angicais da Região de Ribeirão Preto SP usando como ferramenta de análise um conjunto de marcadores moleculares microssatélites (SSR). Para isso, foram construídas duas bibliotecas enriquecidas para microssatélites usando a espécie A. colubrina que resultaram em 20 marcadores SSR testados para a espécie e subsequentemente transferidos para A. peregrina. Desses 20 marcadores, 14 foram polimórficos em cada uma das espécies. Através dessa ferramenta molecular, foi possível realizar os estudos de diversidade genética, endogamia e distribuição genética espacial em A. colubrina e A. peregrina na região de Ribeirão Preto, que acusaram de uma maneira geral, muitas semelhanças entre as duas espécies, bem como entre os angicais de uma mesma espécie. A diferença mais marcante encontrada entre elas foi com relação a estrutura genética espacial, pois todos os angicais de A. colubrina apresentaram forte estruturação, enquanto que os de A. peregrina demonstraram ter uma dispersão aleatória dos indivíduos. O sistema reprodutivo e o fluxo de pólen nas duas espécies foi acessado usando sete marcadores moleculares microssatélites. Para essas análises foram genotipados indivíduos juvenis e adultos (totalizando 352 de A. colubrina e 355 de A. peregrina) presentes nos angicais Acol/PB, Aper/SP255 e Aper/Faz. Através das análises constatou-se que ambas as espécies tem sistema de acasalamento misto, embora A. colubrina tenha apresentado uma proporção maior de autofecundação (tm Acol = 0,619; tm Aper= 0,905). Também foram encontrados elevados índices de cruzamento entre parentes (tm-ts Acol = 0,159; tm-ts Aper = 0,216) e parentesco (coancestria), o que resultou num baixo tamanho efetivo populacional para ambas as espécies. As estimativas das taxas de cruzamentos multilocos individuais apresentaram grande variação nas duas espécies, mostrando a flexibilidade do sistema reprodutivo no gênero Anadenanthera. O número efetivo de doadores de pólen foi muito baixo para um mesmo fruto (1,10 em A. colubrina e 1,24 em A. peregrina) e mais alto entre frutos de uma mesma árvore (2,61 em A. colubrina e 3,35 em A. peregrina), usando a estimativa indireta de correlação de paternidade. Análises de paternidade revelaram distâncias de dispersão de pólen em duas escalas para ambas as espécies. Dessa forma, ocorreram muitos cruzamentos locais, entre árvores próximas no mesmo angical, mas também foram encontradas grandes distâncias de dispersão de pólen. A média da distância de dispersão em A. colubrina foi de 299,88 m e de 214,369 m em A. peregrina. Alto fluxo de pólen oriundo de árvores externas aos angicais de ambas as espécies foi detectado, indicando que os grupos não são isolados reprodutivamente. Por outro lado, o fluxo gênico crítico foi também muito elevado nas estimativas, provavelmente devido ao baixo poder de exclusão que os locos apresentaram dentro dos angicias de ambas as espécies. / Anadenanthera is a genus of Mimosaceae that is endemic to Latin America and the West Indies and comprises two tropical tree species: Anadenanthera colubrina (Vell.) Brenan. (popularly known as angico, angico vermelho, angico branco or curupay) and Anadenanthera peregrina (L.) Speg. (angico, angico preto, angico de casca, angico do cerrado, yopo or cohoba). Both species are commonly found in the Ribeirão Preto region, usually as nearly monospecific agglomerates known as angicais. To aid future conservationist measures, this work investigated the genetic diversity, gene flow, spatial genetic structure and contemporary mating system of A. colubrina and A. peregrina in the angicais of Ribeirão Preto Region SP by analyzing a sample of simple sequence repeat markers (SSR). Two microsatellites libraries were created from A. colubrina, providing 20 SSR markers that were tested for that species and later applied to A. peregrina. Fourteen out of the 20 markers were polymorphic between the species, allowing an examination of the genetic diversity, endogamy and spatial genetic structure in A. colubrina and A. peregrina in the Ribeirão Preto region, which revealed several similarities between the two species, as well as among the angicais of a single species. The most remarkable difference between the species was related to the spatial genetic structure, as all angicais of A. colubrina presented strong structuration, whereas those of A. peregrina exhibited an aleatory dispersion of individuals. The mating system and pollen flow in both species were analyzed through seven SSR. Adults and juveniles from the angicais Acol/PB, Aper/SP255 and Aper/Faz were genotyped for those analyses (352 specimens of A. colubrina and 355 of A. peregrina), revealing that both species undergo a mixed mating system, although A. colubrina presented a higher percentage of self-mating (tm Acol = 0.619; tm Aper= 0.905). High indices of mating among relatives (tm-ts Acol = 0.159; tm-ts Aper = 0.216) and coancestry were also found, resulting in a low effective population size for both species. A wide range in the estimate of the mutilocus breeding rate was found for both species, reflecting the plasticity of the mating system in the genus Anadenanthera. The effective number of pollen donors was very low for a single fruit (1.10 in A. colubrina and 1.24 in A. peregrina) and higher between fruits from the same tree (2.61 in A. colubrina and 3.35 in A. peregrina), using an indirect estimate of the paternity correlation. Paternity analyses revealed the distance of pollen dispersion on two different scales: many local outcrossings (between close trees from the same angical) in addition to long-distance pollen dispersion. The average dispersion distance was 299.88 m in A. colubrina and 214.369 m in A. peregrina. A high pollen flux from trees outside the angicais of both species was observed, indicating a lack of reproductive isolation. However, the gene flow was also very high, likely due to the low power of exclusion presented by loci from both species inside the angicais.

Abstract Genomic clones covering the entire mouse type XIII collagen gene (Col13a1) were isolated, and the complete exon-intron organization was characterized. The gene was found to be about 135 kb in size and to locate in the mouse chromosome 10. Comparison of gene structures and promoter regions between man and mouse indicated high conservation between the two species. In order to understand the biological function of type XIII collagen, a mouse line that expresses type XIII collagen with replacement of the cytosolic and transmembrane domains by a short, non-descript sequence was generated using homologous recombination. Expression of this aminoterminally altered type XIII collagen led to mild but progressive muscular atrophy in mice. The integrity of muscle cells was disturbed and the basement membrane showed areas of detachment from the sarcolemma as well as clearly altered structure at myotendinous junctions. These phenotypical changes were, nevertheless, local, since the majority of the muscle was intact. The results show the importance of the membrane anchorage of the type XIII collagen protein in adhesion and, consequently in the maintenance of muscle integrity. To study the significance of various regions of type XIII collagen, wild-type and mutant forms of the protein were produced recombinantly in insect cells. The transmembrane domain and the adjacent region of ectodomain were found to be crucial for the formation of type XIII collagen molecules with all of the three collagenous domains in trimeric conformation. A previously characterized conserved membrane-proximal region of the ectodomain was predicted to harbour a coiled-coil conformation. This was suggested to begin in the transmembrane domain of type XIII collagen and in several other collagenous transmembrane proteins. Type XIII collagen lacking this coiled-coil sequence was correctly folded with respect to its central COL2 and carboxylterminal COL3 domains. Between them, in the NC3 domain, a second coiled-coil sequence was found, and this was suggested to function as a second association region. The second coiled-coil sequence was found to be conserved in the two other type XIII collagen-like molecules as well. To obtain precise information about the location and level of type XIII collagen expression, a reporter mouse line synthesizing a recombinant protein with the cytoplasmic and transmembrane portions of type XIII collagen linked in-frame with the β-galactosidase enzyme was generated. The reporter mice showed high expression of type XIII collagen at neuromuscular junctions and in the periosteum of bone. Interestingly, the growth of the reporter mice was reduced at puberty. Their long bones showed a decreased diameter and impaired mechanical properties. In addition, their peripheral nerves showed areas of detachment from muscle cells at neuromuscular junctions. These results provide further evidence for the role of type XIII collagen in cell adhesion. They also show the importance of proper adhesion conducted by type XIII collagen in signaling between the extracellular matrix and cells and in the cellular response.

Please read the abstract in the section 00front of this document. / Thesis (PhD)--University of Pretoria, 2010. / Zoology and Entomology / unrestricted

A high proportion of amphibian species are threatened with extinction globally, and habitat loss and degradation are the most frequently implicated causes. Rapid deforestation for the establishment of agricultural production is a primary driver of habitat loss in tropical zones where amphibian diversity is highest. Land-cover change affects native assemblages, in part, through the reduction of habitat area and the reduction of movement among remnant populations. Decreased gene flow contributes to loss of genetic diversity, which limits the ability of local populations to respond to further environmental changes. The focus of this dissertation is on the degree to which common land uses in Sarapiquí, Costa Rica impede the movement of two common amphibian species. First, I used field experiments, including displacement trials, and a behavioral landscape ecology framework to investigate the resistance of pastures to movement of Oophaga pumilio. Results from experiments demonstrate that pastures do impede movement of O. pumilio relative to forest. Microclimatic effects on movement performance as well as limited perceptual ranges likely contribute to reduced return rates through pastures. Next, I linked local processes to landscape scale estimates of resistance. I conducted experiments to measure habitat-specific costs to movement for O. pumilio and Craugastor bransfodrii, and then used experimental results to parameterize connectivity models. Model validation indicated highest support for resistance estimates generated from responses to land-use specific microclimates for both species and to predator encounters for O. pumilio. Finally, I used abundance and experiment-derived resistance estimates to analyze the effects of prevalent land uses on population genetic structure of the two focal species. While O. pumilio did not exhibit a strong response to landscape heterogeneity and was primarily structured by distances among sites, C. bransfordii genetic variation was explained by resistance estimates from abundance and experiment data. Collectivity, this work demonstrates that common land uses can offer different levels of resistance to amphibian movements in Sarapiquí and illustrates the value of investigating local scales processes to inform interpretation of landscape-scale patterns.

Earlier studies investigated the genetic structure of fragmented or isolated elephant populations by comparing the genetic characteristics of pre-defined populations. This study aimed to determine if there was genetic evidence for spatial structuring in a continuous elephant population in the Kavango-Zambezi Transfrontier Conservation Area (KAZA-TFCA). I sequenced one mtDNA gene region for 88 individuals and genotyped 100 individuals for 10 nuclear microsatellite loci. Bayesian Clustering Algorithms incorporated in the program Geneland were used to identify groups of genetically similar individuals. An Analysis of Molecular Variance (AMOVA) determined if these groups (henceforth referred to as subpopulations) were significantly differentiated. I used a Geographic Information System (GIS) landscape genetic toolbox to identify areas in the landscape with high genetic divergence between individual samples to determine if there were identifiable genetic barriers in the landscape. There were three significantly differentiated mtDNA sub-populations (Fst = 0.787), and two nDNA sub-populations that were not significantly differentiated (Fst = -0.02; Rst = -0.045), implying obstructed mtDNA, but high nDNA gene flow across the study region. Also, gene flow was apparent between Chobe and Kafue National Parks, where telemetry data has as of yet not recorded inter-population movements between these parks. The three mtDNA sub-populations were geographically differentiated and followed political boundaries as apparent sub-populations in Botswana, Zambia and Zimbabwe. The differences between mtDNA and nDNA genetic structuring may be explained by i) historical events that shaped the current genetic structure (e.g. through founder-effects and persistent poaching hotspots) and ii) intrinsic variables that influence genetic structure at a local scale (e.g. through resource dependencies and social behaviour). The KAZA elephant population has a genetic diversity (mtDNA diversity as the pairwise number of differences (π) = 2.59; nDNA diversity as the mean alleles/locus and He = 7.5, 0.71) higher than other southern African populations, and inter-population movements may be responsible for maintaining this genetic diversity. I recommend continued support for conservation initiatives that aim at maintaining and restoring connectivity between populations through landscape linkages, which in so doing may ensure inter-population gene flow and uphold the current genetic state of the KAZA-TFCA elephant population. / Dissertation (MSc)--University of Pretoria, 2013. / gm2014 / Zoology and Entomology / unrestricted

Subalpine larch (Larix lyallii Parl.) has a narrow ecological niche at timberline in the Cascade Range and the Rocky Mountains of western North America. Demographic factors, including a long generation time (average 500 years) and a late arrival at sexual maturity (100-200 years), make it unlikely that this species will be able to adapt to predicted climate change. A better understanding of genetic structure and genetic diversity is necessary in order to effectively manage this species for future generations. Foliage from 62 populations of subalpine larch was collected in order to elucidate the range-wide population genomics of the species. DNA was extracted and a next-generation sequencing method, restriction site associated DNA sequencing (RAD-seq), was used to generate genome-wide single nucleotide polymorphism (SNP) marker data. Three genetically differentiated clusters were identified via principal components analysis, a discriminant analysis of principal components and Bayesian STRUCTURE analysis: the Cascade Range, the southern Rocky Mountains and the northern Rocky Mountains. A monophyletic group in the central Rocky Mountains was also identified in a dendrogram of genetic distance but this group had weak bootstrap support (49%), meaning genetic differentiation depends on relatively few genetic variants. Genetically differentiated groups should be prioritized for future management and conservation efforts. Negative values of Tajima’s D and preferred demographic scenarios generated by coalescent simulations indicated that 15 populations all have a recent history of expansion. Genetic diversity within these populations was found to be moderate (HO = 0.15 – 0.20), inbreeding coefficients were found to be high (FIS = 0.15 – 0.25) and genetic differentiation among populations was found to be high (average FST = 0.18). These results indicated that fragmentation driven by Holocene warming may have resulted in reduced effective population sizes. Smaller populations experience stronger genetic drift and an increased likelihood of inbreeding, which may hinder an adaptive response to natural selection. Still, parameter estimates for preferred demographic scenarios suggested a minimum effective population size of around 20,000 individuals, which is not considered small by most conservationists. A final study of 18 populations found local adaptation to cold temperature in the northern portion of the species range. In all seasons, populations from the northern Rocky Mountains had significantly higher cold tolerance than populations from the central Canadian Rocky Mountains and the northern Cascades. Winter cold tolerance showed strong clines associated with the frost-free period and degree days below zero. These two climate variables explained 65% of the explainable variance in phenotype when redundancy analysis models were conditioned on geography. Seven SNPs were identified that explained a significant portion of the variance in winter cold tolerance. Range-wide, additional SNPs were identified as FST outliers and/or as significantly correlated with environmental gradients, even after correcting for neutral genetic structure. Together, the results of this work indicate that dispersal, neutral evolutionary processes and natural selection have all played important roles in shaping patterns of genetic variation across the natural range of subalpine larch. All of these factors should be considered during the development of management and conservation strategies for this high-elevation conifer species. / Graduate

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第18660号 / 農博第2089号 / 新制||農||1028(附属図書館) / 学位論文||H26||N4883(農学部図書室) / 31574 / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 井鷺 裕司, 教授 北島 薫, 教授 北山 兼弘 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Individual variation and fitness are the cornerstones of evolution by natural selection. The trophic niche represents an important source of phenotypic variation on which natural selection can act. Although individual variation is fundamental to species-level ecological and evolutionary change, individual variation is often ignored in population-level approaches to wildlife ecology, conservation and management. Failing to link individual resource use to fitness or to biological outcomes related to fitness limits us to managing for the average resource needs of a population, which may be insufficient for protecting the diversity of resource use within populations and the underlying eco-evolutionary processes that generate that diversity. My goals were to provide insights into the mechanisms that generate and constrain intrapopulation trophic niche variation, evaluate whether linkages exist between individual biological outcomes and variation in food habits across the range of resources consumed within generalist consumer populations and examine how that variation manifests in population-level responses. I investigated the causes and physiological consequences of intrapopulation trophic niche variation in two generalist consumers, the American black bear (Ursus americanus) and brown bear (U. arctos) across three sites in British Columbia, CAN and at one site in Alaska, USA. My primary tools included stable isotope analysis to estimate diet, enzyme-linked immunoassay of hair to quantify the hormone cortisol for indexing physiological stress, and genetic analyses to identify individuals, species, and sex and to estimate ancestry. I found that individual differences in resource use can result in similar biological outcomes and that similar resource use can result in different biological outcomes. Intra- and interspecific competition, sex-based differences in nutritional and social constraints and annual variation in food availability all influenced trophic niche variation and the resultant biological outcomes. I also found evidence of a link between intrapopulation trophic niche variation and population genetic structure. My results highlight the diverse ecological drivers and diverse consequences of trophic niche variation, which further illuminates why the trophic niche is a nexus for eco-evolutionary dynamics.

The effects of landscape structure on wildlife populations have drawn more attention from ecologists and wildlife managers as landscapes have rapidly changed worldwide. The objectives of this study were to (1) conduct a statewide habitat suitability assessment for wild turkeys (Meleagris gallopavo) in Mississippi using machine learning methods; (2) determine landscape-abundance relationships of wild turkeys at 2 spatial scales; and (3) measure genetic distinction of wild turkey populations in Mississippi. I found that habitat suitability for wild turkeys was positively related to amount of forest cover. Wild turkey relative abundance peaked at an optimal hardwood forest proportion of 0.29 and increased with enhanced landscape configuration at the annual dispersal scale, supporting the landscape composition hypothesis. Using microsatellite analysis of 224 birds, I found 3 distinct genetic clusters in Mississippi; however, population genetic differentiation neither fit to the isolation by distance or isolation by resistance models but may have behavioral cues.