Genes are the foundation of evolution and biodiversity. The genetic structure of natural populations needs to be understood to maintain exploited resources rationally. This thesis focuses on genetic variability and methods to determine spatial and temporal genetic heterogeneities. Intense human exploitation generates particular challenges to conserve genetic diversity of fishes since it has genetic effects. My research concerns one of our most valuable fish species: the Atlantic herring (Clupea harengus). I analyzed Atlantic herring samples from the North and Baltic Seas. The objectives were to determine: 1) spatial genetic structure, 2) whether allozymes and microsatellites provide similar descriptions of the differentiation pattern, or 3) if they are influenced by selection, 4) factors affecting statistical power when testing for genetic differentiation, and 5) the temporal stability of the genetic structure. The results show: 1) very low levels of spatial genetic differentiation in Atlantic herring; a major component is a difference between the Baltic and North Seas, 2) a concordant pattern with allozymes and microsatellites, 3) that selection influences a microsatellite locus, which can be a low salinity adaptation, 4) that statistical power is substantial for frequently used sample sizes and markers; the difference in power between organelle and nuclear loci is partly dependent on the populations’ stage of divergence, and 5) no changes in amount of genetic variation or spatial genetic structure over a 24-year period; the selection pattern in one microsatellite locus remained. The notion that the large population sizes make herring unlikely to lose genetic diversity may be disputed. I found small local effective population sizes, and the evidence of selection hints of a distinct evolutionary lineage in the Baltic. When Atlantic herring is managed as very large units, there can be detrimental genetic effects if certain population segments are excessively harvested.

Reintroduction of Anatolian mouflon population at Bozdag Protection &amp / Breeding Station to its former habitats(Emremsultan Wildlife Development Area in Ankara-Nallihan, and Karadag in Karaman) started in 2004. The magnitude of genetic change among Bozdag and reintroduced populations was evaluated by 11 microsatellite loci. Study populations revealed close results (&plusmn / st.dev.) &ndash / Bozdag population: nk = 2.9091 (&plusmn / 1.1362), AE = 2.0250 (&plusmn / 0.9537), Ho = 0.3830 (&plusmn / 0.2717), He = 0.3956 (&plusmn / 0.2746) / Nallihan population: nk = 2.9091 (&plusmn / 1.1362), AE = 2.0592 (&plusmn / 0.9451), Ho = 0.4086 (&plusmn / 0.2977), He = 0.4052 (&plusmn / 0.2767) / and Karadag population: nk = 2.5455 (&plusmn / 1.1282), AE = 1.8809 (&plusmn / 0.8758), Ho = 0.3388 (&plusmn / 0.2775), He = 0.3607 (&plusmn / 0.2716). Population differences for major genetic parameters were not significant (p &gt / 0.05) by comparisons with paired t-test. Also, temporal change in genetic diversity for Bozdag population was investigated by comparison with temporal data. Temporal changes in genetic parameters were found to be not significant and possible causes for differences were argued. Additionally, genetic diversity and PI computations for different traps were verified and compared to uncover any potential bias due to the catching method. Comparisons did not reveal significant differences illustrating the homogeneity among traps. On the other hand, simulations detected the higher sensitivity of allelic diversity (A) to founder events than P and heterozygosity (Ho &amp / He) levels which supports heterozygosity excess method for bottleneck analysis. With the same simulation analysis, observed genetic diversity within reintroduced samples were found to be in the ranges of expectation (99% CI) indicating that translocated individuals were chosen randomly. Bottleneck analysis based on heterozygosity excess method (one-tailed test for heterozygosity excess: pSMM = 0.28515, pTPM = 0.06445, pIAM = 0.02441) and allele frequency distributions method (normal L-shaped) could not detect a recent genetic bottleneck for Bozdag population. However, simulations determined that these two methods are prone to type II error. Bottleneck detection failure for the study population is probably due to type II error instead of other sources of error like violations of model assumptions.

Migration acts as a selective force on the ecology and evolutionary trajectory of species, as well as presenting fundamental challenges for conservation. My thesis examines the impact of migration by exploring patterns of differentiation among and within migratory and non-migratory populations of the Loggerhead Shrike (Lanius ludovicianus). First, I use morphological, genotypic, stable isotope and leg band recovery data to quantify migratory connectivity in the species. Comparison across markers reveals a generally concordant pattern of moderate connectivity to the Gulf Coast, but overall mixing among populations on the wintering grounds. Combining data from multiple markers in a Bayesian framework improves the resolution of assignment of wintering birds to a breeding ground origin. Information on the species’ migratory patterns provides an explicit framework for interpreting patterns of genetic and ecological variation. I test two hypotheses regarding the interaction of gene flow and migratory habit: (1) migration facilitates gene flow; and (2) gene flow will occur most often along the axis of migration. Genetic population structure in migratory populations is weaker than in non-migratory populations, with gene flow facilitated by dispersal movements of females and first year breeders. As predicted, gene flow occurs most often along the north-south axis of migration, likely due either to opportunistic settling of dispersers or potentially, pairing on the wintering grounds. I investigate variation in the extent and scheduling of moult in relation to underlying genetic differences among populations, age, sex, body size, food availability and migratory habit. I find a pattern of interrupted moult across migratory populations, which may represent a trade-off between time allocated to breeding versus molt and migration. Loggerhead Shrikes in eastern and more southerly migratory populations undergo a greater extent of their moult on the breeding grounds and non-migratory individuals undergo a more extensive pre-formative moult than migratory individuals. I interpret this as suggesting a trade-off between resources allocated to molt versus those required for reproduction. / Thesis (Ph.D, Biology) -- Queen's University, 2011-01-25 15:54:36.593

Nothofagus moorei is a long-lived, Gondwana relict cool temperate rainforest tree. Nothofagus-dominated rainforests were widespread across much of eastern Australia during the mid-Tertiary but today, N. moorei occurs only as a series of disjunct, isolated populations in south-east Queensland and northern New South Wales. Clonal regeneration via coppicing is reported to be a common feature of most N. moorei populations, while successful sexual regeneration is believed to be rare, occurring largely only in niches with high light levels and limited competition. While clonal propagation enables population persistence and individual longevity, it cannot generate novel genotypes. Isolated populations, potentially high levels of clonality, low-potential for successful sexual regeneration, long-lived individuals and predicted global warming effects make N. moorei vulnerable to local, if not total, population extinction. The current study aimed to assess the relative conservation status of extant N. moorei populations in order to develop appropriate conservation management strategies for long-term population persistence. Levels of genetic diversity and population structure were examined across the remaining natural distribution of N. moorei using nuclear amplified fragment length polymorphism (AFLP), microsatellite and chloroplast DNA markers. In total 607 individuals were sampled from 20 populations and 5 geographical regions: Lamington/Border Ranges, Ballow, Dorrigo/New England, Werrikimbe and Barrington. Genetic results were then analysed to assess conservation status of each population and geographical region. Microsatellite and AFLP data identified comparatively high levels of genetic diversity in all remnant populations sampled. The prevalence of coppicing in the northern Lamington/Border Ranges populations appears to have had little impact on relative levels of genetic diversity, heterozygosity or population structure. Population differentiation was limited, with the majority of genetic variation retained within populations, no regional structuring and high levels of admixture. Analysis of cpDNA variation showed that the three Dorrigo/New England populations were divergent from all other populations, suggesting an ancient divergence in N. moorei prior to Pleistocene glaciations. While levels of genetic diversity were essentially the same across all populations, Bayesian analysis of genetic structure did identify four populations with differing gene pool proportions which would be important to include in conservation efforts in addition to individuals from other populations. Similarly, individuals from four significantly differentiated groups identified using traditional F-statistics suggests individuals from each of these four groups should be included in future conservation plans. In order to maintain ancient chloroplast lineages, populations from the Dorrigo/New England region should also be assigned special conservation value. Populations of N. moorei appear to have retained significant levels of genetic diversity and show little population divergence in spite of marked reductions in the natural distribution since the Early Miocene. Sampling of these ancient trees however, suggests current levels of diversity in N. moorei actually reflect past diversity and differentiation, and that there have been insufficient generations since the historical contraction in distribution for genetic diversity to be adversely affected and regional differentiation to evolve. Long-term persistence of N. moorei is still threatened by future accelerated climate change and the limited preferred habitat that remains where N. moorei can expand its range. While the ability to regenerate clonally may enable long-term persistence of N. moorei, populations are still likely to continue to decline as climatic conditions will increasingly favour sub-tropical and warm temperate species across much of N. moorei's northern distribution. Southern populations of N. moorei, in contrast, could expand their ranges into eucalypt woodlands as predicted climate becomes warmer and wetter. However, this will ultimately be determined by the frequency of fires, with increased fire frequencies favouring the expansion of eucalypts and contraction and possible local population extinction of N. moorei dominated cool temperate rainforests.

Made available in DSpace on 2014-06-11T19:32:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-02-26Bitstream added on 2014-06-13T19:02:41Z : No. of bitstreams: 1 arruda_mp_dr_sjrp.pdf: 3154075 bytes, checksum: 425658b7ce3ff42cf3fde44c2f7d4d75 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / A destruição e a modificação do hábitat são aceitas, entre os biólogos conservacionistas, como as causas primárias da perda da biodiversidade, e a situação para os anfíbios não é exceção. Diversos processos antropogênicos contribuem para a deterioração das paisagens, podendo afetar negativamente as populações de anfíbios, por alterar fisicamente os ambientes aquáticos e terrestres, reduzindo a conectividade dos hábitats e estruturando as populações. Contudo, poucos dados existem sobre os efeitos do cultivo agrícola para as populações de anfíbios. Os programas de preservação atuam na recuperação de populações ameaçadas e, em geral, estão baseados na manutenção da máxima quantidade de diversidade genética, de tal forma que, a primeira etapa de um programa conservacionista, consiste na avaliação da variabilidade genética e distribuição desta entre as populações. A estruturação gênica populacional dos organismos, estimada a partir de técnicas de biologia molecular é um aspecto fundamental na caracterização da aptidão das espécies aos ambientes. Particularmente os marcadores moleculares do tipo microssatélite tem acessado com êxito a variabilidade gênica das populações. Assim, foram desenvolvidos loci microssatélites polimórficos para as espécies Hypsiboas raniceps, Leptodactylus chaquensis e Rhinella schneideri e avaliada a variabilidade genética de populações provenientes de hábitats com diferentes tipos de perturbação antrópica (práticas agrícolas, pastagem), com o intuito de relacionar o impacto de diferentes matrizes sobre a diversidade genética. A espécie generalista R. schneideri exibiu um estoque uniforme de variabilidade genética, baixa estruturação e reduzido nível de endogamia em todas as populações, sugerindo um elevado potencial de dispersão, responsável pela homogeneização das populações... / The destruction and modification of habitat are accepted between conservation biologists as the primary causes of biodiversity loss, and the situation for amphibians is no exception. Several anthropogenic processes contribute to the deterioration in the landscape, which can adversely affect amphibian populations by physically altering the aquatic and terrestrial environments, reducing the connectivity of habitats and structuring populations. However, few data exist on the effects of the crop for the populations of amphibians. The conservation programs act in the recovery of threatened populations, and generally are based on maintaining the maximum amount of genetic diversity, therefore, the first step in a conservationist program, is to assess the genetic variability and distribution of this among the populations. Population structure of organisms, estimated from molecular biology techniques is fundamental to characterize the fitness of species to environments. Particularly the molecular markers microsatellite has successfully accessed the genetic variability of populations. Therefore, we developed polymorphic microsatellite loci in the Hypsiboas raniceps, Leptodactylus chaquensis and Rhinella schneideri species and evaluated the genetic variability of populations from habitats with different types of anthropogenic disturbance (agricultural practices, pasture), in order to relate the impact of different matrix on genetic diversity. R. schneideri generalist species showed an even amount of genetic variability, low structure and low level of inbreeding in all populations, suggesting a high potential for dispersal, responsible for the homogenization of populations. However, in L. chaquensis and H. raniceps, the populations located in regions with strong agricultural impact (Tietê Batalha) showed genetically depauperate and strong population structure. It can be concluded... (Complete abstract click electronic access below)

Made available in DSpace on 2016-06-02T20:21:26Z (GMT). No. of bitstreams: 1 3627.pdf: 2008232 bytes, checksum: bc522ebd1f078e56d7c127dd1057d56b (MD5) Previous issue date: 2011-03-30 / Financiadora de Estudos e Projetos / The Maned Wolf (Chrysocyon brachyurus) is listed among the threatened extinction species in Brazil due to loss of its natural habitat to agriculture and frequent roadkill. Aiming to determinate the population size of C. brachyurus into a Ecological Station in the northeast of Sao Paulo State (Estação Ecológica do Jataí EEJ), a non invasive method genetic analysis of feces was employed to confirm the specie findings which deposit the feces, in accordance of morphological characteristics and specific scent of the C. brachyurus specie. Through a panel of five loci microsatellite was possible to identify each collected sample. Among the 41 stool samples, we identified 13 specimens of C. brachyurus in the EEJ. The probability of identity (PID) was 0.8 x 10 -6 and the probability of not detecting allelic (allelic dropout) was 16.2%. There was no imbalance linkage between the analyzed loci. Values for C. brachyurus internal heterozygosity were rated low. The observed heterozygosity (Ho) average was 0.52 and expected heterozygosity (He) average was 0.72. The number of alleles per locus was found to be 5.4. In the analysis of Hardy-Weinberg were found three loci that showed some deviations, after Bonferroni correction: loci 2018, 2054 and 2140. Fis values were highly significant for all into the situ population. The degree of relatedness of individuals, or varied of 0.000 (not relative) to 0.5253 (father and son), indicating that there are related animals in the area. Tests conducted to determine the gender of the samples of C. brachyurus were not found satisfactory results, once the expected fragments were not amplified in any of the tests and in none of the samples. The estimation of the population size of the C. brachyurus in the area of EEJ may be used as reference of management action plans of species conservation. / O lobo-guará (Chrysocyon brachyurus) está listado entre as espécies ameaçadas de extinção no Brasil devido à perda de seu hábitat natural para agropecuária e aos freqüentes atropelamentos. Com o objetivo de determinar o número populacional mínimo de C. brachyurus em uma Unidade de Conservação na região nordeste do estado de São Paulo (Estação Ecológica do Jataí EEJ), um método não invasivo de estudo a análise genética de fezes foi utilizado, procurando-se confirmar os achados da espécie que originalmente depositou as fezes de acordo com as características morfológicas e odores característicos e distintivos para a espécie C. brachyurus. Por meio de um painel de 5 locos de microssatélites, foi possível individualizar cada uma das amostras coletadas em campo. Dentre as 41 fezes coletadas, diagnosticamos 13indivíduos de C. brachyurus na EEJ. A probabilidade de identidade (PID) foi de 0,8 x 10 -6 e a probabilidade de não detecção alélica (allelic dropout) de 16,2%. Observou-se ausência de desequilíbrio de ligação entre os locos analisados. Foram encontrados valores baixos de heterozigosidade para C. brachyurus. A heterozigosidade observada (Ho) média foi de 0,52 e a heterozigosidade esperada (He) média foi de 0,72. A média de alelos por loco encontrada foi de 5,4. Nas análises do equilíbrio de Hardy-Weinberg foram encontrados três locos que apresentaram desvios, após a correção de Bonferroni: locos 2018, 2054 e 2140. Os valores de Fis foram significativos para todos os loco na população. Com relação ao grau de parentesco dos indivíduos, o r variou de 0,000 (não parente) até 0,5253 (pai e filho), indicando que há animais relacionados na área. Foram realizados testes para a determinação do sexo das amostras de C. brachyurus, que não demonstraram resultados satisfatórios, uma vez que os fragmentos esperados não foram amplificados em nenhum dos testes realizados e para nenhuma das amostras. A determinação da estimativa do tamanho populacional de C. brachyurus na área da EEJ pode ser utilizada para implantação de planos de manejo e conservação da espécie.

Orientadores: Maria Imaculada Zucchi, Ricardo Ribeiro Rodrigues / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T12:21:20Z (GMT). No. of bitstreams: 1 Schwarcz_KaiserDias_D.pdf: 5972760 bytes, checksum: 6089d106796adfd5fab684651bfb298e (MD5) Previous issue date: 2014 / Resumo: A degradação ecológica e o desflorestamento são processos que se iniciaram há muito tempo e cuja história confunde-se com a da agricultura. A Mata Atlântica é a segunda maior floresta tropical em ocorrência e importância na América do Sul, possuindo grande diversidade biológica e altos níveis de endemismo. A ocupação desordenada da Mata Atlântica causou sua redução a 11,26% de sua área original, com distribuição de forma fragmentada pelo território brasileiro. A destruição da Mata Atlântica tem resultado na eliminação de muitas populações e, potencialmente, na erosão da diversidade genética de diversas espécies. Essa combinação de alto endemismo e forte ameaça de extinção, faz com que a Mata Atlântica seja considerada um hotspot para a conservação. Nas últimas décadas a recuperação de ecossistemas degradados recebeu a atenção da comunidade científica, dando origem ao campo do conhecimento chamado Ecologia da Restauração, que se dedica aos estudos teóricos dos princípios, práticas, resultados e conseqüências de projetos de restauração. O estudo e monitoramento de áreas de restauração florestal é essencial para melhorar as técnicas de restauração em ecossistemas tropicais e subtropicais. Para que uma determinada espécie se perpetue em uma área em processo de restauração, é preciso que a mesma desenvolva todo o seu ciclo de vida e que gerem descendentes capazes de se desenvolver a ponto de substituir as árvores mães quando as mesmas entrarem em senescência. Por isso há a necessidade de se estudar a variabilidade genética de populações arbóreas dentro de áreas de floresta restaurada, assim como a ocorrência e efetividade do fluxo gênico entre estas áreas e os fragmentos de seu entorno. Neste trabalho, estudamos a variabilidade genética de Myroxylon peruiferum L. f., em duas diferentes áreas de restauração florestal e em duas áreas de remanescentes naturais de Floresta Estacional Semidecidual. Nossos resultados indicam que as restaurações florestais de Cosmópolis e Iracemápolis conservam diversidades genéticas HE e alélicas semelhantes às de remanescentes naturais. A principal diferença entre áreas naturais e restauradas foi a menor riqueza de alelos endêmicos nestas últimas o que é um efeito de amostragem que favorece a perda de alelos raros. A área de restauração florestal mais antiga em Cosmópolis apresentou uma estruturação genética espacial compatível com a de áreas naturais. O mesmo não ocorreu com a restauração mais recente de Iracemápolis. Observou-se a ocorrência de estruturação genética local nas áreas naturais e na área de restauração mais antiga e indícios de fluxo gênico entre os áreas nativas e restauradas. Um estudo adicional do efeito de amostragem sobre as freqüências alélicas demonstrou o fenômeno de perda de alelos com baixa freqüência em eventos de amostragem. O mesmo trabalho indicou que uma amostra de cerca de 30 indivíduos é capaz de representar adequadamente alelos com freqüências acima de 0,05; sendo este um bom número a se considerar na seleção de matrizes para fornecimento de mudas para restauração florestal / Abstract: Ecological degradation and deforestation are processes that started long ago and whose history is intertwined with that of agriculture. Atlantic Forest is the second largest rainforest in occurrence and importance in South America, having great biological diversity and high levels of endemism. Disordered occupation of Atlantic Forest caused its reduction to 11.26% of the original area, with distribution in forest fragments poorly conected across the Brazilian territory. Destruction of the Atlantic Forest has resulted in the elimination of many populations and potentially the erosion of genetic diversity of several species. This combination of high endemism and strong threat of extinction causes the Atlantic Forest to be considered a hotspot for conservation. In the last decades recovery of degraded ecosystems has received attention from the scientific community giving birth to an new area of knowledge called the Restoration Ecology. The study and monitoring of areas of forest restoration is essential to improve restoration techniques in tropical and subtropical ecosystems. For a given species to perpetuate itself in an area undergoing a restoration process, it needs to develop its whole life cycle and generates progeny capable of developing to the point of replacing mothers trees when they die. Therefore there is a need to study the genetic variability of tree populations within areas of restored forest, as well as the occurrence and effectiveness of gene flow between these areas and surrounding fragments. We studied the genetic variability of Myroxylon peruiferum L. f., in two different areas of forest restoration and in two areas of natural remnants of semideciduous forest. Our results indicates that restorations in Cosmopolis and Iracemápolis conserve genetic and allelic diversity HE similar to that of natural remnants. The main difference between natural and restored areas was the lowest richness of endemic alleles which is the result of a sampling effect that favors the loss of rare alleles. The area of older forest restoration in Cosmopolis presented a spatial genetic structure consistent with natural areas. This did not occur with the newer restoration in Iracemápolis. We observed the occurrence of local genetic structure in natural areas and in the area of older restoration and evidence of gene flow between native and restored areas. An additional study about the effect of sampling size on allele frequencies showed the phenomenon of loss of low frequency alleles in sampling events. The same study found that a sample of about 30 individuals are able to adequately represent alleles with frequencies above 0.05; this is a good number to consider in selecting matrix trees to supply seedlings for forest restoration / Doutorado / Genetica Vegetal e Melhoramento / Doutor em Genetica e Biologia Molecular

Landscape genetic approaches allow to study effects of landscape to population microevolution. Landscape can influence gene flow even in large carnivores with good dispersal ability. Understanding the influence of landscape to the gene flow between populations is crucial for species conservation, especially in the species with low population densities. Aim of the study was to describe genetic structure of the grey wolf (Canis lupus) and snow leopard (Panthera uncia) in selected areas and to determine the influence of the landscape features on observed structure. Non-invasive genetic samples of snow leopard from Nepal were analysed, as well as invasive and non-invasive samples of grey wolf from Central Europe. Population structure was determined a posteriori using Bayesian clustering approaches that integrate genetic and geographical data, and compared to landscape connectivity models. Population structure of snow leopards is mostly influenced by human presence and presence of frequented roads, which represent a substantial dispersal barrier. Habitat suitable for this species is greatly restricted by altitude, however, during dispersal they are able to overcome areas with higher elevation than what is optimal for them. Pronounced genetic difference was found between central European and Carpathian...

No description available.

<p dir="ltr">The Blanding’s Turtle (<i>Emydoidea blandingii</i>) is a species of conservation needs that ranges across the U.S Midwest and Northeast, and Ontario/Nova Scotia, Canada. The species has experienced several range expansions and contractions due to glacial dynamics and industrial landscape changes, which have led to population isolation and bottlenecks. Understanding genetic variation and population structure across the species’ geographic range is essential for conservation efforts to maintain and restore populations. While several regional studies have evaluated genetic variation in <i>E. blandingii</i>, there has been little population sampling across Michigan and limited attempts to directly compare genetic variation across extensively sampled populations within both its main range and disjunct segments in the Northeast U.S. In this study, I utilized 12 microsatellite loci to directly compare the genetic diversity of <i>E. blandingii</i> across 153 localities in a portion of the Great Lakes and the Northeast of the range. Additionally, 13 microsatellite loci were used to assess genetic diversity across 92 localities in Indiana, Ohio, and Michigan, including further sampling within Michigan. My findings confirmed higher genetic diversity within the Great Lakes compared to the Northeast and revealed greater genetic differentiation in the Northeast than in the Great Lakes. Population structure in both regions was influenced by distance (IBD) and watersheds, with a more pronounced effect in the Northeast. Using four different genetic clustering approaches (PCA, sPCA, STRUCTURE, and TESS3r), I identified three range-wide clusters, three within the Northeast, and three within the Great Lakes. Within the Great Lakes, estimates of effective population size (<i>N</i>e) were high at both the population and watershed level, although influenced by sample size. The long lifespans of <i>E. blandingii</i> likely contribute to high levels of genetic diversity, while post-glacial gene flow across the landscape has resulted in low to moderate levels of differentiation within the regions. This study highlights poorly understood population structure and differences in genetic diversity between regions. Although Great Lakes populations are less isolated and more genetically diverse than those in the Northeast, this does not suggest that they are secure. Both regions face potential genetic loss over the next century, requiring further management implications to mitigate any further decline.</p>