The genetic structure of 26 natural populations of three species (S. tridecemlineatus, S. mexicanus, and S. spilosoma) of the Ictidomys subgenus of ground squirrels was analyzed using chromosomal and electrophoretic techniques. Chromosomal variation was not observed in S. mexicanus, and only slight karyotypic variation was found in the other two species. Chromosomal evidence indicated hybridization between S. tridecemlineatus and S. mexicanus, placing these species within the classical definition of semispecies. Analysis of electrophoretic variation at 29 genetic loci indicated close genetic relationships between these species. Evolution in Ictidomys appears to be linked with Pleistocene events, and speciation appears to have occurred within the last 155,000 years.

Orientador: Miguel Luiz Menezes Freitas / Resumo: Este estudo teve como finalidade conhecer a diversidade genética de duas populações de Hevea brasiliensis, conservadas ex situ em Selvíria-MS e Marabá-PA, bem como estimar os parâmetros genéticos e medidas de dissimilaridade de suas progênies. Foram utilizados15 locos microssatélites para investigar a diversidade e estrutura genética e o parentesco de 18 matrizes da POP SEL e 46 da POP MAB. No ano de 2016, foi instalado em Selvíria-MS um teste de progênies a partir de sementes das referidas matrizes. As progênies foram avaliadas por meio de cinco variáveis silviculturais e oito morfológicas. A população de Selvíria apresentou número total de alelos (100) menor do que a população Marabá (179), com a média por locos de 6,7 e 11,9, respectivamente. A heterozigosidade esperada (He ), heterozigosidade observada ( Ho) e o índice de fixação (F) foram semelhantes entre populações, mas a riqueza alélica (R ) foi maior em Selvíria. A diferenciação genética entre as populações ( = 0,28) revelou que 72% da diversidade genética está distribuída dentro das populações. O coeficiente médio de coancestria dentro de ambas as populações foi positivo, mas os valores foram próximos de zero (< 0,08) e considerando indivíduos de ambas as populações, a coancestria media foi zero (-0,001). A estimativa de parâmetros genéticos utilizando o modelo linear misto univariado aditivo REML/BLUP, demonstrou que a herdabilidade individual não foi significativa para a maioria das variáveis observadas nas progên... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: This study aimed to know the diversity, genetic structure and kinship of genotypes of two populations of Hevea brasiliensis, conserved ex situ in Selvíria-MS and Marabá-PA, as well as to evaluate the genetic parameters and measures of dissimilarity of their progenies. 15 microsatellite loci were used to investigate the diversity and genetic structure and kinship of 18 matrices from Selvíria-MS and 46 from Marabá-PA. In the year 2016, a progeny test was installed in Selvíria-MS from seeds of said matrices. The progenies were evaluated by means of five silvicultural variables and eight morphological variables. The population of Selvíria presented a total number of alleles (100) smaller than the Marabá population (179) with the average per locos of 6,7 and 11,9 respectively. The expected heterozygosity (eH), observed heterozygosity (oH) and fixation index (F) were similar among populations, but allelic richness (R) was higher in Selvíria. Genetic differentiation among populations (Gst = 0.28) revealed that 72% of genetic diversity is distributed within populations. The mean coefficient of coancestria within both populations was positive, but values were close to zero (<0.08) and considering individuals from both populations, mean covensis was zero (-0.001). The univariate mixed linear additive model methodology REML / BLUP showed that the individual heritability parameter was not significant for most of the variables observed in the progenies. However, they presented mean herita... (Complete abstract click electronic access below) / Doutor

<p>The identification of processes governing genetic structure at different spatial scales remains a major challenge in evolutionary biology and is of considerable applied interest in conservation biology. In <i>Euphrasia stricta</i> five varieties have been identified (<i>brevipila</i>, <i>gotlandica</i>, <i>stricta</i>, <i>suecica</i> and <i>tenuis</i>) based on differences in habitat, phenology and morphology. In this thesis, I examined genetic variation at AFLP and microsatellite marker loci in relation to variation in habitat and morphology within and among varieties of <i>E. stricta</i> on the island Gotland in the Baltic Sea. The results are discussed in relation to evolutionary processes acting within this species complex. </p><p>In a study conducted at the regional scale, the two early-flowering varieties <i>suecica</i> and <i>tenuis</i> each formed a genetically distinct group, while the three late-flowering varieties <i>brevipila</i>, <i>gotlandica</i> and <i>stricta</i> formed a third group. The results suggest that <i>suecica</i> and <i>tenuis</i> have ancient origins since they are genetically different both from the <i>brevipila</i>/<i>gotlandica</i>/<i>stricta</i> group and from each other despite their similar habitat preferences. This pattern was obtained using both marker systems. Discrepancies between AFLP and microsatellites were found in patterns of isolation by distance and in estimates of expected heterozygosity, <i>H</i>_e.</p><p>Focusing on the mixed genetic group <i>brevipila</i>/<i>gotlandica</i>/<i>stricta</i> and the causes behind their clustering together despite differences in morphology and habitat preferences, I performed a study at a smaller geographic scale. Studying a population of <i>E. stricta</i> I found that, although gene flow within the population was strong, it had not prevented the formation of genetic groups associated with micro-habitat properties. </p><p>An important result for conservation of the rare variety <i>suecica</i> is its distinct genetic separation from variety <i>tenuis</i>. If the aim of conservation is to preserve the uniqueness of <i>suecica,</i> the two varieties should be treated as separated entities. </p>

The identification of processes governing genetic structure at different spatial scales remains a major challenge in evolutionary biology and is of considerable applied interest in conservation biology. In Euphrasia stricta five varieties have been identified (brevipila, gotlandica, stricta, suecica and tenuis) based on differences in habitat, phenology and morphology. In this thesis, I examined genetic variation at AFLP and microsatellite marker loci in relation to variation in habitat and morphology within and among varieties of E. stricta on the island Gotland in the Baltic Sea. The results are discussed in relation to evolutionary processes acting within this species complex. In a study conducted at the regional scale, the two early-flowering varieties suecica and tenuis each formed a genetically distinct group, while the three late-flowering varieties brevipila, gotlandica and stricta formed a third group. The results suggest that suecica and tenuis have ancient origins since they are genetically different both from the brevipila/gotlandica/stricta group and from each other despite their similar habitat preferences. This pattern was obtained using both marker systems. Discrepancies between AFLP and microsatellites were found in patterns of isolation by distance and in estimates of expected heterozygosity, He. Focusing on the mixed genetic group brevipila/gotlandica/stricta and the causes behind their clustering together despite differences in morphology and habitat preferences, I performed a study at a smaller geographic scale. Studying a population of E. stricta I found that, although gene flow within the population was strong, it had not prevented the formation of genetic groups associated with micro-habitat properties. An important result for conservation of the rare variety suecica is its distinct genetic separation from variety tenuis. If the aim of conservation is to preserve the uniqueness of suecica, the two varieties should be treated as separated entities.

Cichlid fishes from the East African Rift lakes Victoria, Tanganyika and Malawi represent a preeminent example of replicated and rapid evolutionary radiation. In this single natural system, numerous morphological (eg. jaw and tooth shape, color patterns, visual sensitivity), behavioral (eg. bower-building) and physiological (eg. development, neural patterning) phenotypes have emerged, much akin to a mutagenic screen. This dissertation encompasses three studies that seek to decipher the underpinnings of such rapid evolutionary diversification, investigated via the genetic variation in East African cichlids. We generated a valuable cichlid genomic resource of five low-coverage Lake Malawi cichlid genomes, from which the general properties of the genome were characterized. Nucleotide diversity of Malawi cichlids was low at 0.26%, and a sample genotyping study found that biallelic polymorphisms segregate widely throughout the Malawi species flock, making each species a mosaic of ancestrally polymorphic genomes. A second genotyping study expanded our evolutionary analysis to cover the entire East African cichlid radiation, where we found that more than 40% of single nucleotide polymorphisms (SNPs) were ancestral polymorphisms shared across multiple lakes. Bayesian analysis of genetic structure in the data supported the hypothesis that riverine species had contributed significantly to the genomes of Malawi cichlids and that Lake Malawi cichlids are not monophyletic. Both genotyping studies also identified interesting loci involved in important sensory as well as developmental pathways that were well differentiated between species and lineages. We also investigated cichlid genetic variation in relation to the evolution of microRNA regulation, and found that divergent selection on miRNA target sites may have led to differential gene expression, which contributed to the diversification of cichlid species. Overall, the patterns of cichlid genetic variation seem to be dominated by the phenomena of extensive sharing of ancestral polymorphisms. We thus believe that standing genetic variation in the form of ancestrally inherited polymorphisms, as opposed to variations arising from new mutations, provides much of the genetic diversity on which selection acts, allowing for the rapid and repeated adaptive radiation of East African cichlids.

Population Genetics has led to countless numbers of fruitful studies of evolution, due to its abilities for prediction and description of the most important evolutionary processes such as mutation, genetic drift and selection. The field is still growing today, with new methods and models being developed to answer questions of evolutionary relevance and to lift the veil on the past of all life forms. In this thesis, I present a modest contribution to the growth of population genetics. I investigate different questions related to the dynamics of populations, with particular focus on studying human evolution. I derive an upper bound and a lower bound for FST, a classical measure of population differentiation, as functions of the homozygosity in each of the two studied populations, and apply the result to discuss observed differentiation levels between human populations. I introduce a new criterion, the Gain of Informativeness for Assignment, to help us decide whether two genetic markers should be combined into a haplotype marker and improve the assignment of individuals to a panel of reference populations. Applying the method on SNP data for French, German and Swiss individuals, I show how haplotypes can lead to better assignment results when they are supervised by GIA. I also derive the population size over time as a function of the densities of cumulative coalescent times, show the robustness of this result to the number of loci as well as the sample size, and together with a simple algorithm of gene-genealogy inference, apply the method on low recombining regions of the human genome for four worldwide populations. I recover previously observed population size shapes, as well as uncover an early divergence of the Yoruba population from the non-African populations, suggesting ancient population structure on the African continent prior to the Out-of-Africa event. Finally, I present a case study of human adaptation to an arsenic-rich environment.

The larger grain borer (LGB) Prostephanus truncatus (Horn) is the most important pest of farm stored maize and cassava in Africa. This alien invasive species was introduced into the continent from Mesoamerica in the late 1970s and by 2008 had spread to at least 18 countries. In contrast to indigenous primary storage pests, LGB exists as on-farm and as wild populations, hence, sustainable control must target both environments. Biological control is especially attractive for wild populations to reduce early season grain store infestation, while cultural and chemical methods are useful to protect stored produce directly. Two populations of the predator Teretrius nigrescens Lewis were introduced into several African countries' as a biocontrol agent. It has shown long-term success and cost effective control in warm-humid areas. Control has however not been successful in cool and hot-dry zones. The aim of this study was to investigate the possible underlying genetic and ecological explanations for these observations and the possibility of joint use of molecular markers and ecological parameters in the development of sustainable control strategies. A 28-month baseline monitoring and recovery activity was done in from 2004 in five regions in Kenya along an east-westerly transect. Monitoring and live sample collection was also done in the original outbreak area in eastern Kenya. There was greater LGB flight activity in western Kenya (high potential maize production area) than the low potential areas. Very few T. nigrescens were recovered, solely in the eastern regions. LGB flight activity followed a seasonal pattern mostly related to changes in the relative humidity at 12:00, rainfall and dew point temperature but with a 3 - 4 week lag. A linear predictive model based on these factors predicted 27 % of the observed flight activity. The survival and predation of five strains of T. nigrescens were compared at eight temperature levels between 15 °C and 36 °C at low and high humidity. All the strains of T. nigrescens exerted a significant reduction of LGB population build-up between 21 °C and 33 °C with generally better performance under humid conditions. There was no evidence of T. nigrescens development at 15 °C. At 18 °C, T. nigrescens oviposition and development was observed but the effect on LGB did not differ significantly from the control. The KARI population was the least effective in preventing grain damage at lower temperatures, but performed better than other strains above 30 °C at low humidity conditions. There was no control at 18 °C and 36 °C under both high and low humidity conditions. Since the extent of genetic differentiation in T. nigrescens was unclear from prior studies, several molecular marker techniques were progressively used. The RAPD-PCR did not reveal any genetic diversity between geographical populations. A 1000bp region of the mitochondrial mtCOI gene revealed two distinct clades differing consistently at 26 segregating sites. The two clades can be identified by simple PCR-RFLP procedure using single or double sequential restriction with EcoR1, HincII, RsaI and DdeI digestion. However, the two lineages co-exist among the mid-altitude Central American populations. The internal transcribed spacer regions ITS1 and ITS2 with some neighbouring coding sequences of the ribosomal DNA were cloned and sequenced. The spacer regions were so variable in length and sequence between T. nigrescens and related Histeridae species that direct sequence alignment was not meaningful. Within T. nigrescens, there was intragenomic variability of the spacer regions mostly involving insertions and deletions of variable tandem repeat units predominantly within the ITS regions. The short flanking coding (18S, 5.8S and 21S) regions were conserved across populations and six other Histeridae species. There was no significant secondary structure variation of the ITS regions among populations of T. nigrescens. Twenty-four novel variable microsatellite markers were developed and tested on the Honduras populations. Alleles per locus ranged between two and twelve with observed heterozygosity between 0.048 and 0.646. Six loci deviated significantly from Hardy Weinberg Equilibrium and possibly had null alleles. The success of microsatellite amplification in outgroup species and variability of markers declined with an increase in the phylogenetic distance between the test species and T. nigrescens. Genotyping 432 individuals from 13 geographic populations revealed a comparatively higher genetic diversity in field populations. Partial isolation by distance and time was observed. Population bottlenecks were not detected, but recent expansion was evident in laboratory populations. Although five dominant genetic clusters were identified by Bayesian methods, meaningful hierarchical population structure was observed at between two and nine population groups (p < 0.01; 10,000 iterations). Biological control of the larger grain borer using T. nigrescens seems an important aspect of the sustainable integrated control approach of the pest. Ecological adaptations, appropriate release strategies and genetic diversity are all essential considerations in these efforts and could be responsible for the variable success already observed. There is some genetic differentiation between populations of T. nigrescens but, further studies would be necessary to ascertain the contribution of such diversity to its predatory performance. The effect of laboratory culturing in aggravating genetic drift should be accommodated to avoid loss of diversity during sampling, quarantine, rearing and release of the predator. / Thesis (Ph.D. (Environmental Science))--North-West University, Potchefstroom Campus, 2009.

The larger grain borer (LGB) Prostephanus truncatus (Horn) is the most important pest of farm stored maize and cassava in Africa. This alien invasive species was introduced into the continent from Mesoamerica in the late 1970s and by 2008 had spread to at least 18 countries. In contrast to indigenous primary storage pests, LGB exists as on-farm and as wild populations, hence, sustainable control must target both environments. Biological control is especially attractive for wild populations to reduce early season grain store infestation, while cultural and chemical methods are useful to protect stored produce directly. Two populations of the predator Teretrius nigrescens Lewis were introduced into several African countries' as a biocontrol agent. It has shown long-term success and cost effective control in warm-humid areas. Control has however not been successful in cool and hot-dry zones. The aim of this study was to investigate the possible underlying genetic and ecological explanations for these observations and the possibility of joint use of molecular markers and ecological parameters in the development of sustainable control strategies. A 28-month baseline monitoring and recovery activity was done in from 2004 in five regions in Kenya along an east-westerly transect. Monitoring and live sample collection was also done in the original outbreak area in eastern Kenya. There was greater LGB flight activity in western Kenya (high potential maize production area) than the low potential areas. Very few T. nigrescens were recovered, solely in the eastern regions. LGB flight activity followed a seasonal pattern mostly related to changes in the relative humidity at 12:00, rainfall and dew point temperature but with a 3 - 4 week lag. A linear predictive model based on these factors predicted 27 % of the observed flight activity. The survival and predation of five strains of T. nigrescens were compared at eight temperature levels between 15 °C and 36 °C at low and high humidity. All the strains of T. nigrescens exerted a significant reduction of LGB population build-up between 21 °C and 33 °C with generally better performance under humid conditions. There was no evidence of T. nigrescens development at 15 °C. At 18 °C, T. nigrescens oviposition and development was observed but the effect on LGB did not differ significantly from the control. The KARI population was the least effective in preventing grain damage at lower temperatures, but performed better than other strains above 30 °C at low humidity conditions. There was no control at 18 °C and 36 °C under both high and low humidity conditions. Since the extent of genetic differentiation in T. nigrescens was unclear from prior studies, several molecular marker techniques were progressively used. The RAPD-PCR did not reveal any genetic diversity between geographical populations. A 1000bp region of the mitochondrial mtCOI gene revealed two distinct clades differing consistently at 26 segregating sites. The two clades can be identified by simple PCR-RFLP procedure using single or double sequential restriction with EcoR1, HincII, RsaI and DdeI digestion. However, the two lineages co-exist among the mid-altitude Central American populations. The internal transcribed spacer regions ITS1 and ITS2 with some neighbouring coding sequences of the ribosomal DNA were cloned and sequenced. The spacer regions were so variable in length and sequence between T. nigrescens and related Histeridae species that direct sequence alignment was not meaningful. Within T. nigrescens, there was intragenomic variability of the spacer regions mostly involving insertions and deletions of variable tandem repeat units predominantly within the ITS regions. The short flanking coding (18S, 5.8S and 21S) regions were conserved across populations and six other Histeridae species. There was no significant secondary structure variation of the ITS regions among populations of T. nigrescens. Twenty-four novel variable microsatellite markers were developed and tested on the Honduras populations. Alleles per locus ranged between two and twelve with observed heterozygosity between 0.048 and 0.646. Six loci deviated significantly from Hardy Weinberg Equilibrium and possibly had null alleles. The success of microsatellite amplification in outgroup species and variability of markers declined with an increase in the phylogenetic distance between the test species and T. nigrescens. Genotyping 432 individuals from 13 geographic populations revealed a comparatively higher genetic diversity in field populations. Partial isolation by distance and time was observed. Population bottlenecks were not detected, but recent expansion was evident in laboratory populations. Although five dominant genetic clusters were identified by Bayesian methods, meaningful hierarchical population structure was observed at between two and nine population groups (p < 0.01; 10,000 iterations). Biological control of the larger grain borer using T. nigrescens seems an important aspect of the sustainable integrated control approach of the pest. Ecological adaptations, appropriate release strategies and genetic diversity are all essential considerations in these efforts and could be responsible for the variable success already observed. There is some genetic differentiation between populations of T. nigrescens but, further studies would be necessary to ascertain the contribution of such diversity to its predatory performance. The effect of laboratory culturing in aggravating genetic drift should be accommodated to avoid loss of diversity during sampling, quarantine, rearing and release of the predator. / Thesis (Ph.D. (Environmental Science))--North-West University, Potchefstroom Campus, 2009.

Southern pine beetle (SPB), Dendroctonus frontalis (Zimmerman), is one of the most destructive insect pests of pine trees in southern United States, Mexico and Central America. There is relatively little information on the effect of habitat fragmentation on the connectivity and the spatial population genetics of SPB. This study therefore, adds to previously generated information by assessing how habitat fragmentation affects the spatial population genetic structure of SPB. It also introduces a new approach to the study of bark beetle population dynamics by assessing how landscape variables shape their effective dispersal. To address this issue, a suite of eight highly polymorphic DNA microsatellite markers were used to measure SPB movement over a representative range of SPB habitat and non-habitat (matrix). At the broadest scale, highly significant genetic differentiation suggests that the sampled populations are not panmictic. Loci with higher variability yielded higher resolution for both the infinite allele model based measure of differentiation (FST) and the stepwise mutation based measure (RST) estimates. It is apparent that allelic frequency differences, allelic size ranges and repeat motif played a role in the observed patterns of pair-wise differentiations between the sampled localities. It is supposed that gene flow, wide-range dispersal and recent divergent time could have contributed to the lower level of genetic structure observed in the pair wise estimates. The sampled populations did not show any differentiation attributable to the host species from which they were collected. Mantel test of genetic distance and Euclidean geographic distance revealed no correlation. Mantel tests of the correlation between genetic distance and cost weighted Euclidean distances also suggest that dispersal of SPB across geographic barriers is not significantly reduced. Thus, landscape features and host preference do not appear to have had an impact on population genetic structure of SPB. Since movements of these beetles were not significantly hindered by environmental factors like major rivers, roads, elevation and host type, it is advisable for regional pest management offices to put an effort and coordinate their prevention and management plans in a broader scale to alleviate the problem associated with this native insect pest. Disequilibrium in the observed homogenized pattern of the beetle in this study suggests human contribution in the dispersal of SPB. Therefore, stringent control is deemed necessary in transportation of logs. This could improve our pest management system hence its positive implication in timber industry is obvious.

Rodovias podem fragmentar populações por dois mecanismos, mortalidade e evitamento. Como espécies que evitam rodovias são raramente atropeladas por veículos e, então, não são detectadas em monitoramentos de fauna atropelada, outras abordagens são necessárias para identificar se eles estão sendo afetados. Ctenomys minutus (tuco-tuco) é um roedor subterrâneo que habita campos arenosos nas margens de rodovias e são raramente registrados em monitoramentos de fauna atropelada. Buscamos identificar se as rodovias são uma barreira para o fluxo gênico de tuco-tuco baseado em nove loci de microssatélite. Coletamos amostras de tecido epitelial de indivíduos de quatro populações: duas com a presença (Weber e Amaral) e, como controle, duas com a ausência de rodovia (Maribo I e Maribo II). Mensuramos diversidade genética, diferenciação genética (estatística F) e acessamos estrutura genética (agrupamento bayesiano). Não observamos redução na variabilidade genética e encontramos um baixo nível de isolamento entre Weber e Amaral e um isolamento ainda menor entre Maribo I e Maribo II. O método bayesiano separou os indivíduos em dois grupos, onde Maribo I e Maribo II são um grupo consistente e Weber e Amaral possuem fracas diferenciações. Os resultados nos indicam que um efeito de barreira entre as populações separadas pela rodovia está em processo e que é necessário mais tempo para observarmos de forma mais clara o isolamento. São necessários mais estudos genéticos e comportamentais para certificar este padrão. Sob aspectos práticos, seria adequado monitorar as populações afetadas e, eventualmente, aplicar alguma medida de mitigação na estrada pra proporcionar conectividade. Por fim, a abordagem genética se mostrou muito interessante para avaliar este impacto. / Roads can fragment populations by two mechanisms, mortality and avoidance behavior. Since species that avoid roads are rarely killed by vehicles and thus cannot be detected in roadkill surveys, other approaches are necessary to identify whether they are affected. Ctenomys minutus (tuco-tuco) is a subterranean rodent who inhabits sand fields including at the margins of roads, however is rarely recorded on roadkill surveys. We aimed to identify if roads are a barrier to the gene flow of tuco-tuco based on nine microsatellite loci. We collected tissue samples from individuals of four populations: a pair with the presence (Weber and Amaral) and, as control, a pair with absence of a road (Maribo I and Maribo II). We measured the genetic diversity, the genetic differentiation (F-statistics), and assessed the genetic structure (Bayesian clustering). We observed no reduction in genetic variability and a low isolation level in pairwise comparison of Weber and Amaral, which was even lower between Maribo I and Maribo II. The Bayesian method separated individuals into 2 clusters, where Maribo I and Maribo II are one consistent cluster and Weber and Amaral present weak differentiations. The results indicate that a barrier effect between populations separated by roads is in process. More genetic and behavioral studies are needed to confirm this pattern. Under practical aspects, it would be appropriate to monitor the affected populations and possibly apply some mitigation measure on the road to provide connectivity. Finally, genetic approach proved very interesting to evaluate this impact.