Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Large-scale human-mediated movements of organisms promote the establishment of species outside their native ranges and a very small proportion of these species become invasive. Invasive species management typically assumes that introduced species are single, static evolutionary units that are genetically analogous to their native counterparts. However, studies have shown that native and introduced populations of a number of introduced plants differ vastly in their genetic composition. These differences may negatively affect the overall success of control and management programmes, particularly for species that are intra-specifically diverse. The influence of intra-specific diversity on the invasion process was tested in two widely exported tree species that are native to Western Australia, Acacia saligna (three subspecies) and Paraserianthes lophantha (two subspecies). Climate matching between the native and introduced range (using species distribution models, SDM) is widely used to forecast future invasion risks, however, it is unknown if SDMs can detect intra-specific niche differences in invasive plants. The SDMs I developed for the subspecies of A. saligna detected intra-specific differences within the native range, but did not predict the full invasive distribution in South Africa. Unsurprisingly, SDMs agreed with genetic analyses (based on nuclear microsatellites, nuclear DNA, and chloroplast DNA) and did not assign South African populations to any subspecies of A. saligna. South African populations were assigned to a novel genetic entity likely produced by human cultivation practices. A global phylogeny identified this cultivated genotype in introduced populations in eastern Australia and Portugal, while the remaining introduced populations differed markedly in their genetic composition. Overall, A. saligna‘s high intra-specific diversity and complex introduction history generated a variety of genetic patterns across the current global distribution of the taxon. Global populations of P. lophantha were processed using a similar approach to that used for A. saligna, and aimed to determine if the same pathways and modes of introduction produced analogous genetic patterns in a closely related species. Diverse arrays of genotypes were identified in introduced populations of P. lophantha, suggesting inconsistent sampling of a variety of native sources. Further work is however needed to clarify the morphological and genetic differences (if any) between the intra-specific entities, and identify exactly which P. lophantha subspecies were introduced outside of their native range, The variation in the global distribution of genetic diversity observed in A. saligna and P.lophantha demonstrated that intra-specific genetic variation, human usage, and the pathway and manner of introduction interact during several phases of the invasion process and collectively determine the introduced genetic patterns. The dissimilarity in the distribution of genotypes in both species suggests that they might not behave the same way throughout their introduced range. Consequently, management insights might not be transferrable between regions. More generally, my findings provide an important contribution to the debate whether (and how quickly) introduced and native populations should be treated as fundamentally different entities. / AFRIKAANSE OPSOMMING: Grootskaalse menslike verskuiwing van organismes bevorder die vestiging van spesies buite hul natuurlike voorkomsareas en 'n klein hoeveelheid van hierdie spesies word indringers. Tydens die bestuur van indringerspesies word dit tipies aanvaar dat ingevoerde indringerspesies enkele, statiese evolusionêre eenhede is wat analoog is aan hul inhmeemse eweknieë. Studies het egter getoon dat inheemse en uitheemse populasies van 'n aantal ingevoerde plante aansienlik verskil in hul genetiese samestelling. Hierdie verskille kan 'n negatiewe invloed op die algehele sukses van beheer- en bestuursprojekte hê, veral vir die spesies wat intra-spesifiek divers is. Die invloed van intra-spesifieke diversiteit op die indringingsproses is getoets aan twee boomspesies, inheems aan Wes-Australië, wat wyd uitgevoer word: Acacia saligna (drie subspesies) en Paraserianthes lophantha (twee subspesies). Vergelyking van klimaatstoestande tussen n spesie se in- en uitheemse voorkomsareas word wyd gebruik om toekomstige indringingsrisiko te voorspel. Dit was voor hierdie navorsing onduidelik of spesie verspreiding modelle (SVMs) intra-spesifieke nis-verskille in indringerplante kan uitwys. SVMs wat vir die subspesies van A. saligna ontwikkel is, kon intra-spesifieke verskille in Wes-Australië uitwys, maar het nie die volle verspreiding van die spesies in Suid-Afrika voorspel nie. Onverbasend, is geen Suid-Afrikaanse populasies deur genetiese analise (gebaseer op die kern mikrosatelliete, kern-DNS, en chloroplas-DNS) toegewys aan 'n subspesie van A. Saligna nie. Suid-Afrikaanse populasies het 'n nuwe genetiese entiteit wat waarskynlik gekweek is deur menslike verbouingspraktyke. 'n Globale filogenie het hierdie verboude genotipe in addisionele ingevoerde populasies in die ooste van Australië en Portugal geïdentifiseer. Mikrosatelliet genotipes van uitheemse populasies wêreldwyd in Oos-Australië, Israel, Italië, Nieu-Seeland, Portugal, Suid-Afrika, Spanje en die VSA verskil merkbaar in hul genetiese samestelling. A. saligna se hoë intra-spesifieke diversiteit en komplekse geskiedenis van invoer (wat verbouing, wye verspreiding en hoë ―propagule druk betrek), het 'n verskeidenheid van genetiese patrone oor die huidige globale verspreiding van die takson gegenereer. Om te bepaal of 'n globale uiteenlopende genetiese patroon binne nouverwante spesies bestaan, is globale bevolkings van Paraserianthes lophantha verwerk deur gebruik te maak van 'n soortgelyke benadering as wat vir A. saligna gebruik is. Globale populasies van beide studie-spesies bestaan uit 'n diverse verskeidenheid van genotipes. Resultate dui daarop dat P. lophantha van 'n verskeidenheid inheemse bronne ingevoer is. Om te identifiseer watter P. lophantha subspesies buite hul natuurlike voorkomsarea versprei is, word verdere werk benodig om die morfologiese en genetiese verskille (indien enige) tussen die intra-spesifieke entiteite vas te stel. In hierdie tesis het ek gewys dat intra-spesifieke genetiese variasie, menslike gebruik en invoering-geskiedenis saam werk om genetiese patrone in uitheemse populasies te vorm. Verder het ek die waarde van die gebruik van verskillende molekulêre benaderings om indringing geskiedenis te verstaan, gedemonstreer. Die verskil in die verspreiding van die genotipes van A. saligna en P. lophantha dui daarop dat hulle moontlik nie op dieselfde manier dwarsdeur hul uitheemse verspreidingsarea mag optree nie. Bestuursinsigte mag gevolglik nie oordraagbaar wees tussen streke nie. Meer algemeen, bied my bevindings 'n belangrike bydrae tot die debat of (en hoe vinnig) inheemse en ingevoerde populasies behandel moet word as fundamenteel verskillende entiteite.

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

The field slug Deroceras reticulatum is a major pest in UK agriculture and amidst growing concern and regulatory pressures surrounding chemical molluscicides, innovation is required to advance the current repertoire of slug controls. This study set out to investigate the bacteria associated with D. reticulatum to assess their importance to the slug and potential as a target for biological control. Slug gut bacterial isolates identified using the phenotypical API system (BioMérieux) and 16S rRNA gene sequencing, were mainly soil-dwelling organisms of the phyla Proteobacteria and Bacteriodetes some of which may be important in human or plant disease. A ribosomal intergenic spacer analysis (RISA) was developed to study microbial communities in the slug gut. Slugs had an average species richness of 12 and comparing the bacterial communities in slugs from different locations yielded a mean similarity of 0.159 (Jaccard index) which was significantly lower than similarity indices of slugs collected within a single location (Mean Jaccard index 0.205, p<0.001, ANOVA). Cloning and sequencing of RISA bands common to slugs and slug eggs, but absent from the surrounding soil and plants identified bacteria for future investigation as potential beneficial symbionts. Bacteria extracted from the slug gut were tested for sensitivity to 16 antibiotics and greatest inhibition of growth was observed for chloramphenicol, gentamicin and tetracycline. These antibiotics administered to slugs by feeding and injection caused a reduction in gut-associated bacteria in plate counts, and in bacterial 16S rDNA quantities estimated by real-time quantitative PCR. Field collected D. reticulatum has a large transient gut bacterial population which is reduced upon starvation to a low background level. No significant detrimental effect of antibiotic treatment on the fitness and survival of the slugs was seen, in some instances control slugs suffered greater mortality than slugs that had been injected with antibiotic. Slugs that died during bioassays had a significantly greater amount of bacterial 16S rDNA in their gut than slugs that were sacrificed as healthy individuals suggesting the presence of a bacterial pathogen. This study has found little evidence that a bacterial symbiont may exist and be important for optimal fitness and survival of D. reticulatum, but insight into slug associated bacteria will be valuable in the direction of future studies in this field.

Rhinichthys osculus (Cyprinidae), the speckled dace, is the most widely distributed freshwater fish in the western United States. The southern California populations of R. osculus are identified as the Santa Ana speckled dace (SASD), though the SASD has not yet been formally recognized as a distinct taxon. Current mtDNA analysis performed in the Metcalf Lab has shown a reciprocally monophyletic relationship among three California regions; southern, central coast, and Owens Valley. Similarly, microsatellite genotyping has shown significant levels of geographic population structure. The purpose of this study was to provide nuclear DNA sequence data to determine the taxonomic status of the SASD to elucidate their evolutionary history and the relationships among the three regions, and to further define their evolutionary trajectory by comparing SASD sequence data to that of speckled dace from the Colorado River of Arizona. To examine this, three EPIC intron markers were sequenced on 54 samples representing all four regions. Based on the mtDNA and microsatellite data alone, there is strong support that the southern California populations of R. osculus are a reproductively isolated taxon at the species level. My study confirms this by showing the SASD to be reciprocally monophyletic for nuclear DNA markers, in conjunction with the mitochondrial DNA marker analyses. Because they are evolutionarily independent and face increased incidence of drought, fire, and flood, endangered species status should be considered.

Marine mammals comprise a paraphyletic group of species whose current abundance and distribution has been greatly shaped by past environmental changes and anthropogenic impacts. This thesis describes molecular ecological approaches to answer questions regarding habitat requirements, genetic differentiation, and life-history trade-offs in three species of marine mammals.  The annual sea-ice dynamics of the Arctic may have large effects on the abundance and distribution of Arctic species such as the pagophilic ringed seal (Pusa hispida). Paper I describes and applies a simple molecular method for isolating and characterizing a relatively large set of single nucleotide polymorphisms (SNPs) in the ringed seal. These SNPs have been genotyped in a yet-to-be-analysed dataset which will form the basis in an assessment of the micro-evolutionary effects of annual sea-ice dynamics on ringed seal.  Current management efforts directed towards the North Atlantic fin whale (Balaenoptera physalus) are hampered by an unclear understanding of population structure. Paper II investigates the DNA basis for the high levels of genetic differentiation that have been reported in allozyme studies of the North Atlantic fin whale. We find that additional processes (at the organismal level) may have contributed to shaping the phenotype of the underlying allozyme variation. Telomeres may potentially serve as markers for determining the chronological and biological age of animals where other means of inference is difficult. Paper III describes the application and evaluation of four qPCR assays for telomere length estimation in humpback whales (Megaptera novaeangliae), finding that reliable telomere length estimates require extensive quality control. Paper IV applies the best performing qPCR assay to test whether telomeres may provide a method for genetic determination of chronological age in whales and concludes that the biological and experimental variation in telomere length estimates is too large to determine age with sufficient resolution. Finally, because telomere length and rate of telomere loss also may be affected by other cellular and organismal processes, such as resource allocation among self-maintenance mechanisms, growth and reproduction, Paper V describes the correlations between individual telomere length and rate of telomere loss, and sex, maturity status and female reproductive output. We found that the costs of reproduction in terms of telomere loss are higher in mature humpback whales than in juveniles; that reproductive costs are higher in males than females; and that differences among females tend to correlate with reproductive output. / At the time of doctoral defence the following papers were unpublished and had a status as follows: Paper 2: Submitted; Paper 3:Submitted; Paper 4: Manuscript; Paper 5:Manuscript

Speciation is an important process that is responsible for the generation of biodiversity on Earth. The importance of gene flow during speciation is hotly debated; however, it can be investigated by studying the process of intraspecific population differentiation. Here, I investigate the mechanisms that influence population differentiation and gene flow in brown (Sula leucogaster) and red-footed boobies (S. sula). These species are congeneric, broadly sympatric, and ecologically similar; however, they differ in their marine habitat preference (inshore vs. pelagic). I hypothesized that: (i) gene flow is restricted by major physical barriers in both species, and (ii) gene flow in the absence of physical barriers is more prevalent in red-footed boobies due to their pelagic marine habitat preference. First, I characterized the structure and function of the booby mitochondrial genome. Using extensive DNA sequencing and phylogenetic methods, I found that boobies have tandemly duplicated mitochondrial control regions that evolve in concert. I suggest that concerted evolution of duplicated control region may be common in seabirds. To quantify matrilineal population genetic structure and gene flow, I sequenced one control region in 513 brown and red-footed boobies. Both species exhibited strong population genetic structure that was attributable to continental barriers to gene flow such as the Isthmus of Panama. In the absence of physical barriers, gene flow was more prevalent in red-footed boobies. I also used microsatellite and nuclear intron loci to perform multilocus phylogeographic analyses of brown and red-footed boobies. Individuals of both species could be grouped into four genetic populations that corresponded to oceanographic regions. In red-footed boobies, gene flow following secondary contact of previously isolated lineages was common, perhaps due to a pelagic habitat preference. In brown boobies, major genetic populations apparently diverged in the absence of gene flow. Despite this, Isla San Benedicto in the Eastern Pacific is a site of secondary contact between brown booby lineages that diverged approximately one million years ago, and hybrids are apparently fertile. These findings suggest that gene flow following secondary contact may be an important, but overlooked, component of speciation. / Thesis (Ph.D, Biology) -- Queen's University, 2012-04-28 17:28:53.302

Orientador: Sergio Nascimento Stampar / Resumo: O estudo da conectividade entre as populações é de grande relevância para entender como variantes ambientais podem afetar estes eventos, reconhecendo os padrões de estrutura genética e filogeográficos. Grande parte das espécies marinhas possuem, ao menos, uma fase larval com alto potencial de dispersão, onde possivelmente possa resultar numa população homogênea e com maior conectividade, comparado a outros grupos de animais. Para a compreensão dos padrões variáveis, as análises moleculares trazem informações importantes sobre a variabilidade genética, evolução e mudanças demográficas na história. Por este motivo torna-se cada vez mais importante o uso destes dados em pesquisas que abordam conceitos populacionais. Os acompanhamentos dos cenários em organismos planctônicos ainda são escassos, mesmo com sua grande abundância no ambiente marinho. Sob o cenário da representativa espécie de medusa, endêmica do Atlântico Sul Ocidental, Lychnorhiza lucerna Haeckel 1880 (Scyphozoa; Rhizostomeae) diante de lacunas ainda existentes sobre a estrutura populacional foi analisado como as populações estão se comportando geneticamente ao longo de toda sua distribuição e para isto foram utilizados os marcadores COI, ITS-1 e 2 para inferir a divergência intra e inter-populacional. Os resultados obtidos indicaram um padrão histórico de alta conectividade entre as subpopulações de Lychnorhiza lucerna evidenciando a existência de uma Metapopulação em grande escala. / Abstract: The study of connectivity between populations is relevant to understand the environmental diversity impact on the populations, acknowledging both genetic structural and phylogeographic patterns. Most of the marine species exhibit at least one larval stage with a high dispersal potential that possibly results in a homogeneous population with a wide connectivity when compared to other groups of animals. Molecular analysis provide essential informations concerning the genetic variability, evolution and demographic changes along the history supporting the recognition of variable patterns. Thus, it is essential the use of these data in researches approaching population concepts. Even though planktonic organisms are very abundant in the marine environment, studies regarding the scenario comprising these organisms are scarce. Owing to existing gaps about that, populations of the remarkable medusa specie endemic in the South Western Atlantic, Lychnorhiza lucerna Haeckel 1880 (Scyphozoa; Rhizostomeae), were genetically assessed along the geographic distribution known . For this were used COI and ITS 1-2 molecular markers to conclude about intrapopulation/ interpopulation divergence. The results obteined indicated a historic pattern of high connectivity between subpopulations of Lychnorhiza lucerna evidencing a metapopulation existence on a large scale. / Mestre

Submitted by Stefany Archangelo de Angelis null (stefany.archangelis@hotmail.com) on 2018-03-13T14:41:37Z No. of bitstreams: 1 VERSÃO ficha catalografica_DISSERTAÇÃO STEFANY_OK.pdf: 2022875 bytes, checksum: 3f24d2ef22761a31bf2d4ab1b1d18584 (MD5) / Rejected by Disleide Silvia Valerio Gounella null (disleide@clp.unesp.br), reason: Boa tarde. Favor corrigir e completar os itens: - O nome do arquivo deve ser o título do trabalho; - Incluir palavras-chaves em inglês; - Incluir abstract; - Folha de aprovação com data. - As referência bibliográficas foram feitas baseadas nas Normas da ABNT? ABS. Disleide Silvia Valerio Gounella Bibliotecária CLP - São Vicente Fone: (13)3569-7154 Mailto: disleide@clp.unesp.br skype: disleidesilviavaleriogounella on 2018-03-15T18:32:55Z (GMT) / Submitted by Stefany Archangelo de Angelis null (stefany.archangelis@hotmail.com) on 2018-03-16T01:25:44Z No. of bitstreams: 1 Conectividade Populacional de Lychnorhiza lucerna (Cnidaria; Scyphozoa) no Atlântico Sul.pdf: 3463809 bytes, checksum: 5c128c22ffece0245d8284e53a0c5430 (MD5) / Rejected by Disleide Silvia Valerio Gounella null (disleide@clp.unesp.br), reason: xxxxxxxxxxxxxxxxxxxx on 2018-03-19T20:05:54Z (GMT) / Submitted by Stefany Archangelo de Angelis null (stefany.archangelis@hotmail.com) on 2018-03-19T20:07:48Z No. of bitstreams: 1 Conectividade Populacional de Lychnorhiza lucerna (Cnidaria; Scyphozoa) no Atlântico Sul.pdf: 3463809 bytes, checksum: 5c128c22ffece0245d8284e53a0c5430 (MD5) / Approved for entry into archive by Disleide Silvia Valerio Gounella null (disleide@clp.unesp.br) on 2018-03-19T20:26:56Z (GMT) No. of bitstreams: 1 angelis_sa_me_svic.pdf: 3463809 bytes, checksum: 5c128c22ffece0245d8284e53a0c5430 (MD5) / Made available in DSpace on 2018-03-19T20:26:56Z (GMT). No. of bitstreams: 1 angelis_sa_me_svic.pdf: 3463809 bytes, checksum: 5c128c22ffece0245d8284e53a0c5430 (MD5) Previous issue date: 2018-02-19 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O estudo da conectividade entre as populações é de grande relevância para entender como variantes ambientais podem afetar estes eventos, reconhecendo os padrões de estrutura genética e filogeográficos. Grande parte das espécies marinhas possuem, ao menos, uma fase larval com alto potencial de dispersão, onde possivelmente possa resultar numa população homogênea e com maior conectividade, comparado a outros grupos de animais. Para a compreensão dos padrões variáveis, as análises moleculares trazem informações importantes sobre a variabilidade genética, evolução e mudanças demográficas na história. Por este motivo torna-se cada vez mais importante o uso destes dados em pesquisas que abordam conceitos populacionais. Os acompanhamentos dos cenários em organismos planctônicos ainda são escassos, mesmo com sua grande abundância no ambiente marinho. Sob o cenário da representativa espécie de medusa, endêmica do Atlântico Sul Ocidental, Lychnorhiza lucerna Haeckel 1880 (Scyphozoa; Rhizostomeae) diante de lacunas ainda existentes sobre a estrutura populacional foi analisado como as populações estão se comportando geneticamente ao longo de toda sua distribuição e para isto foram utilizados os marcadores COI, ITS-1 e 2 para inferir a divergência intra e inter-populacional. Os resultados obtidos indicaram um padrão histórico de alta conectividade entre as subpopulações de Lychnorhiza lucerna evidenciando a existência de uma Metapopulação em grande escala. / The study of connectivity between populations is relevant to understand the environmental diversity impact on the populations, acknowledging both genetic structural and phylogeographic patterns. Most of the marine species exhibit at least one larval stage with a high dispersal potential that possibly results in a homogeneous population with a wide connectivity when compared to other groups of animals. Molecular analysis provide essential informations concerning the genetic variability, evolution and demographic changes along the history supporting the recognition of variable patterns. Thus, it is essential the use of these data in researches approaching population concepts. Even though planktonic organisms are very abundant in the marine environment, studies regarding the scenario comprising these organisms are scarce. Owing to existing gaps about that, populations of the remarkable medusa specie endemic in the South Western Atlantic, Lychnorhiza lucerna Haeckel 1880 (Scyphozoa; Rhizostomeae), were genetically assessed along the geographic distribution known . For this were used COI and ITS 1-2 molecular markers to conclude about intrapopulation/ interpopulation divergence. The results obteined indicated a historic pattern of high connectivity between subpopulations of Lychnorhiza lucerna evidencing a metapopulation existence on a large scale.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2015-01-16T17:09:06Z No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Monik Oprea - 2013.pdf: 1967380 bytes, checksum: 406bdd6925672cd697798a30f89bc4d5 (MD5) / Approved for entry into archive by Erika Demachki (erikademachki@gmail.com) on 2015-01-16T17:32:35Z (GMT) No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Monik Oprea - 2013.pdf: 1967380 bytes, checksum: 406bdd6925672cd697798a30f89bc4d5 (MD5) / Made available in DSpace on 2015-01-16T17:32:35Z (GMT). No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Monik Oprea - 2013.pdf: 1967380 bytes, checksum: 406bdd6925672cd697798a30f89bc4d5 (MD5) Previous issue date: 2013-06-19 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Microsatellite markers are important tools for molecular ecology studies, particularly for bats, whose information is difficult to obtain through direct observations. In the first chapter, we conducted searches for scientific articles about the use of microsatellite markers in bats in order to evaluate the current knowledge about the genetic patterns and also to unravel sociological aspects of this knowledge. We found that the use of microsatellite markers to study bats is quite new and little spread. Many questions in molecular ecology can be addressed with a limited number of polymorphic markers, such as microsatellites. This will not only contribute to the knowledge of the species biology, but also to design effective strategies for conservation of bat species. In the second chapter, we report the development and characterization of ten microsatellite loci for the bat Glossophaga soricina isolated from a shotgun genomic library. Among 67 individuals, the number of alleles per locus ranged from 2 to 20, and the observed and expected heterozygosity ranged from 0.015 to 0.606 and from 0.016 to 0.915, respectively. The high combined probability of genetic identity (4.369x10-8) and probability of paternity exclusion (0.996) showed that the microsatellite loci are useful for population genetic structure and detailed parentage studies in natural populations of G. soricina. In the third chapter, we used the nine developed microsatellite loci and spatially explicit analysis to unravel population genetic structure and how landscape features affected genetic diversity of G. soricina at 17 localities in the Brazilian Cerrado. Our results showed that G. soricina populations already have higher inbreeding in fragmented landscapes in small geographic scales. Also, some pairs of populations showed genetic discontinuity as the outcome of landscape modification. / Marcadores microssatélites são ferramentas importantes para estudos de ecologia molecular, principalmente para estudos sobre morcegos, cujas informações são difíceis de acessar através de observações diretas. No primeiro capítulo, buscamos artigos científicos sobre o uso de microssatélites em morcegos para avaliar o conhecimento atual dos padrões genéticos e revelar os aspectos sociológicos desse conhecimento. Nós observamos que o uso de marcadores microssatélites é relativamente recente e ainda pouco difundido. Muitas questões em ecologia molecular poderiam ser respondidas com um número limitado de marcadores moleculares, como os microssatélites. Isso não só contribuiria para o conhecimento da biologia, mas também para desenhar estratégias efetivas para conservação das espécies de morcegos. No segundo capítulo, apresentamos o desenvolvimento e caracterização de dez locos de microssatélites para o morcego Glossophaga soricina, isolados a partir de uma biblioteca shotgun. Foram analisados os genótipos de 67 indivíduos, sendo que o número de alelos por locos variou de 2 a 20, e a heterozigozidade observada e esperada variaram entre 0.015 a 0.606 e entre 0.016 a 0.915, respectivamente. A alta probabilidade de identidade genética (4.369x10-8) e a probabilidade de exclusão de paternidade (0.996) mostraram que os locos de microssatélites desenvolvidos são úteis para estudos de estrutura genética e paternidade em populações naturais de G. soricina. No terceiro capítulo, foram usados nove locos de microssatélites desenvolvidos, juntamente com análises espacialmente explícitas para acessar a estrutura genética, e verificar como as características da paisagem afetam a diversidade genética de G. soricina em 17 localidades do Cerrado brasileiro. Nossos resultados mostraram que populações de G. soricina já apresentam altos índices de endogamia em paisagens fragmentadas em pequenas escalas geográficas. Além disso, alguns pares de populações apresentaram descontinuidade genética como resultado da modificação da paisagem.

Although the “genome as a blueprint” metaphor has been pervasive in biology, recent advances in molecular biology have revealed a complex network of regulatory machinery that dynamically regulated molecular processes in response to environmental conditions. However, these patterns, as well as the evolutionary processes that underlie them, remain understudied in natural conditions. In 2010, the Deepwater Horizon oil spill released an estimated 4.9 million barrels of oil into the Gulf of Mexico, making landfall on salt marsh habitat dominated by the foundation species Spartina alterniflora. Despite the severe impacts to phenotype and fitness, S. alterniflora proved remarkably resilient in the face of the crude oil stress. Despite the tragedy of the Deepwater Horizon oil spill, the event represented a unique opportunity to explore the molecular mechanisms of oil tolerance in this highly resilient species. To understand how organisms regulate gene expression in natural settings and to identify best practices in genome-wide expression studies, we first surveyed a ten-year span of transcriptome-wide gene expression studies. We then confirmed the hypothesis that crude oil exposure would induce differential gene expression in affected populations, and whole-transcriptome microarray identified 3,622 genes that responded exclusively to oil stress. To confirm the function of candidate genes involved in resilience to oil stress, we used a highly-differentially expressed subset of these genes to construct gene interaction networks and identify target genes. We obtained T-DNA insertion genotypes of the emerging model grass species Brachypodium distachyon that were disrupted in these target genes for functional confirmation, but were unable to detect significant modulation of oil response through these heterologous knockouts. Finally, we isolated the phenotypic effects of crude oil exposure through greenhouse trials and found evidence that crude oil may have acted as a selective pressure, rather than an inducer of plasticity. Together, these studies identify novel patterns of gene expression in response to a severe but unpredictable stressor that has widespread impacts on a foundational salt marsh grass species. In addition, this dissertation represents a pathway to understanding functional genomics in non-model systems without extensive genomic resources.