La consanguinité est connue par les biologistes pour diminuer la valeur sélective des individus en diminuant par exemple leur survie ou leur fertilité. De ce fait, la sélection naturelle devrait favoriser l'apparition de comportements permettant l'évitement des accouplements entre apparentes pour limiter les conséquences néfastes dues à la dépression de consanguinité. Cette dépression de consanguinité est particulièrement visible chez les Hyménoptères avec un système de détermination du sexe appelé single-locus Complementary Sex Determination (sl-CSD), où elle amène à la production de males diploïdes non viables ou stériles. Mon travail de thèse a ainsi consiste à étudier le phénomène d'évitement d'accouplements entre apparentes dans des populations naturelles d'un hyménoptère parasitoïde avec sl-CSD, Venturia canescens, ainsi que des signaux utilisés par les femelles pour déterminer l'apparentement qu'elles ont avec les individus qu'elles rencontrent. Nous avons d'abord étudié le lien unissant type d'habitat (continental, iles ou laboratoire), diversité génétique et production de males diploïdes dans 11 populations de V. canescens. En effet, un cadre théorique nomme "Vortex d'extinction du aux males diploïdes" prédit une corrélation négative entre isolations des populations, diversité génétique et production de males diploïdes pouvant amener à l'extinction de populations d'Hyménoptères. Nous avons ainsi démontré une corrélation négative entre diversité génétique et production de males diploïdes dans les populations isolées de V. canescens. Ensuite, il a été montré précédemment que les femelles de cette espèce étaient capables de discriminer les males qui leur étaient apparentes et d'éviter les accouplements entre apparentes en laboratoire. Nous nous sommes ainsi intéressés à ce phénomène d'évitement d'accouplement entre apparentes dans des populations naturelles grâce au génotypage de 450 individus du terrain et leur descendants. Nous avons montré que les femelles toléraient les accouplements entre apparentes sur le terrain ainsi qu'en laboratoire en présence de plusieurs males, nous permettant de mettre en lumière l'importance des conditions environnementales sur le choix du partenaire sexuel. Nous nous sommes enfin concentrés sur le système de reconnaissance des apparentes au niveau mécanistique en étudiant les signaux chimiques utilisés par les femelles pour reconnaitre leurs apparentes dans deux contextes écologiques différents, le choix du partenaire sexuel et l'évitement du superparasitisme lors de la ponte. Nous avons ainsi montré des similitudes entre les compositions chimiques de ces deux signaux mais aussi qu'ils n'étaient pas interchangeables entre les deux contextes écologiques étudiés. Au final, les résultats obtenus apportent un nouvel éclairage sur les conditions nécessaires à l'apparition d'un évitement d'accouplements entre apparentes dans des populations naturelles ainsi que sur les signaux utilisés lors de la reconnaissance de parentèle chez un hyménoptère parasitoïde / Inbreeding is well known by biologists to lower the fitness of individuals by or example decreasing survival or fertility. Therefore, natural selection should favour behaviours preventing the reproduction of genetically-related individuals or mitigating harmful consequences, called inbreeding depression. Inbreeding depression is particularly visible in Hymenoptera with a sex-determination system called single-locus Complementary Sex Determination (sl-CSD), where it leads to the production of diploid males that are either unviable or sterile. My PhD work has thus been devoted to the study of sib-mating avoidance in natural populations of a parasitoid with sl-CSD, Venturia canescens, and to understand the cues used by females recognize their kin. We first studied the link between habitat type (continental, island or captive), genetic diversity and diploid male production in 11 V. canescens populations. Indeed, a theoretical framework called "Diploid male extinction vortex" predict a negative correlation between populations’ isolation, genetic diversity and diploid male production that could lead to the extinction of hymenopteran populations.We actually showed a negative correlation between genetic diversity and diploid male production in isolated populations. Previous studies have furthermore demonstrated kin discrimination and sib-mating avoidance by V. canescens females in the laboratory. We therefore studied the sibmating avoidance behaviour in natural populations of this species by genotyping more than 450 wild individuals and their offsprings. We demonstrated that females tolerated inbreeding in the wild as well as in the laboratory when several males were present. We highlighted the importance of environmental conditions on mate choice. At last, we were interested in the kin recognition system and researched the chemical cues used by females in two ecological contexts, mate choice and superparasitism avoidance. This allowed us to identify similarities in the composition of the two chemical signals and that they were not interchangeable between the two studied ecological contexts. In the end, the results we obtained shed new light on the necessary conditions for the apparition of sib-mating avoidance in natural populations, as well as on the cues used for kin recognition in a parasitoid

Habitat fragmentation is one of the main threats to semi-natural grasslands all over Europe, causing reductions in both numbers of populations and numbers of individuals withinpopulations. Small isolated populations are particularly vulnerable to fluctuations that reducespopulation size and could lead to loss of genetic variation due to inbreeding depression, orfixation of harmful alleles due to genetic drift. The aim of this study was to investigate if thecritically endangered eyebright Euphrasia stricta var. suecica experiences pollen limitation,inbreeding depression and heterosis or outbreeding depression. Low pollen limitation waspredicted as well as low inbreeding depression due to high selfing rate. Outbreedingdepression or heterosis was expected based on previous studies indicating strong geneticdifferentiation among populations. This study was conducted in two traditionally managedmeadows in the central part of Gotland, Sweden, using supplemental hand-pollinations andcontrolled crosses. Individuals were collected when the flowering period was over and seedswere counted and weighed. There were no signs of either pollen limitation, inbreedingdepression, heterosis or outbreeding depression in any of the two wooded hay meadows. Thedegree of autonomous selfing was high, indicating that E. stricta var. suecica is not dependenton pollinators for seed production. A significant difference between the meadows was foundin proportion of viable seeds. As there were no signs of local adaptation, individuals could betranslocated between the two studied populations or seed sowings could be used to increasepopulation size. However, before such conservation efforts are undertaken, it is important toconduct further studies that investigate several populations including more life-stages.

Orientadora: Profa. Dra. Cibele Biondo / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Evolução e Diversidade, São Bernardo do Campo, 2018. / A queixada (Tayassu pecari) é uma espécie considerada vulnerável globalmente e criticamente ameaçada em áreas de Mata Atlântica, devido à pressão de caça e fragmentação de habitat. A fragmentação de habitat devido a atividades antrópicas pode acarretar em estruturação genética das populações, além perda de diversidade genética e aumento de endogamia, o que pode contribuir para o processo de extinção local. O presente estudo teve como objetivo estimar o status genético da população de queixadas da região do Pontal do Paranapanema, na Mata Atlântica de SP. Essa região foi altamente fragmentada por atividades antrópicas e, no momento da realização da amostragem para este trabalho, a espécie se encontrava em apenas três dos fragmentos remanescentes (Parque Estadual do Morro do Diabo ¿ PEMD, Fazenda Ponte Branca ¿ FPB e Fazenda Santa Mônica ¿ FSM). Atualmente, é considerada extinta na região. Foram analisadas 47 amostras de sangue, coletadas entre os anos de 1999 e 2005, que foram genotipadas para 11 locos de microssatélites. Observou-se uma estruturação genética das três localidades amostradas em duas subpopulações. Duas das três localidades foram agrupadas em uma única subpopulação (PEMD e FPB) e houve diferenciação genética significativa apenas entre duas delas (PEMD e FSM). Os índices de diversidade genética foram similares para as três localidades e não foram encontradas evidências significativas de endogamia. Esses resultados podem ser explicados de duas formas: 1) existência de fluxo gênico, mesmo que baixo, entre as localidades amostradas (principalmente entre PEMD e FPB); 2) diferenciação recente das subpopulações. Conforme esperado para populações fragmentadas, houve evidências de gargalo populacional recente nas três localidades. Os resultados aqui obtidos podem ser indicativos do papel da paisagem antropizada na estruturação de populações de queixadas mesmo em pequena escala, já que o mesmo não tem sido registrado para regiões mais conservadas. Desta forma, estas evidências podem servir de direcionamento para planos de manejos e ações conservacionistas para outras populações de queixadas que se encontram em condições semelhantes a esta, visando diminuir as chances de extinção local em outras regiões. / The white-lipped peccary (Tayassu pecari) is considered vulnerable throughout its distribution and it is critically endangered in the Atlantic Forest, due to hunting pressure and habitat fragmentation. Habitat fragmentation caused by anthropic activities usually lead to population genetic structure, loss of genetic diversity and higher levels of inbreeding, which contributes to local extinctions. In this study, we addressed the genetic status of a white-lipped peccary population from Pontal do Paranapanema region, located in the Atlantic Forest of São Paulo State in Brazil. This area was highly fragmented by anthropic activities and white-lipped peccaries were found only in three remnant fragments (Parque Estadual do Morro do Diabo ¿ PEMD, Fazenda Ponte Branca ¿ FPB e Fazenda Santa Mônica ¿ FSM) when they were sampled for this work. Currently, they are considered extinct in the region. A total of 47 blood samples were collected between 1999 and 2005 and were genotyped for 11 microsatellite loci. We found that the three fragments sampled were structured in two subpopulations, with two of them being grouped into a single subpopulation (PEMD and FPB). We observed significant genetic differentiation only between two fragments (PEMD and FSM). The genetic diversity indices were similar for the three fragments and no indicators of inbreeding were found. These results can be explained in two ways: 1) existence of gene flow, even if low, between fragments (mainly between PEMD and FPB); 2) recent differentiation of the subpopulations. As expected for fragmentated populations, we found evidence of a population bottleneck for all the fragments sampled. These results can be indicative of the role of anthropized landscape in the structuration of white-lipped peccary populations even on a small scale, since it has not been recorded for well conserved regions. These finds can serve to delineate management plans and conservation actions for other white-lipped peccary populations that are in similar conditions, aiming to reduce the chances of local extinction in other regions.

Orientador: Mario Luiz Teixeira de Moraes / Resumo: As espécies florestais possuem grande importância econômica, pois oferecem diversos produtos fundamentais para a sociedade, mas dada a impossibilidade de se separar ações de melhoramento das de conservação de recursos genéticos, técnicas como os testes combinados de progênies e procedências, tanto para espécies exóticas ou nativas, visam a seleção de árvores pelo valor genético e a transformação dos experimentos em PSM (pomares de semente por mudas). Os pomares de sementes são os vetores de produção de sementes de alta qualidade genética, que ligam as atividades de melhoramento das árvores às práticas de conservação. No anterior contexto, sementes de polinização aberta provenientes de uma população base de Eucalyptus camaldulensis e de um fragmento de Cerrado com Hymenaea stigonocarpa, foram coletadas e plantadas na Faculdade de Engenharia de Ilha Solteira (FEIS/UNESP), em Selvíria-MS. O objetivo deste trabalho foi verificar a variação genética e ganhos genéticos a partir do desbaste dentro de progênies de E. camaldulensis aos 10 anos de idade e estimar parâmetros genéticos populacionais, por meio de marcadores moleculares do tipo microssatélites para H. stigonocarpa, com vistas ao melhoramento genético e conservação, respectivamente. Para análise quantitativa, os caracteres altura (ALT), diâmetro a altura do peito (DAP), volume (VOL), densidade básica (DBM) e sobrevivência (SOB) foram utilizados. Assim os valores observados para sobrevivência (>90%) de E. camaldulensis indic... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Forest species are of great economic importance, as they offer several fundamental products for society, but given the impossibility of separating actions to improve those from the conservation of genetic resources, techniques such as the combined testing of progenies and provenances for both exotic and native species, aim at the selection of trees by their genetic value and the transformation of the experiments in PSM (seed orchards by seedlings). Seed orchards are the vectors of seed production of high genetic quality, which link tree improvement activities to conservation practices. In the previous context, open pollination seeds from a base population of Eucalyptus camaldulensis and a fragment of Cerrado with Hymenaea stigonocarpa, were collected and planted at the Faculty of Engineering of Ilha Solteira (FEIS/UNESP), in Selvíria-MS. The objective of this work was to evaluate the genetic variation and genetic gains from thinning within E. camaldulensis progeny at 10 years of age, and to estimate population genetic parameters, using microsatellite molecular markers for H. stigonocarpa, with a view to genetic improvement and conservation, respectively. For quantitative analysis, the characters height (H), diameter at breast height (DBH), volume (VOL), basic density (DBM) and survival (SUR) were used, thus the values observed for survival (> 90%) indicate good adaptation of the species to the place. Estimates considered to be of high magnitude were obtained for the coefficie... (Complete abstract click electronic access below) / Doutor

The European ground squirrel (Spermophilus citellus) (hereinafter EGS) is under the Law on Nature Protection and is included as a critically endangered into the Red List of Endangered Species. In the Czech Republic, which represents the northwestern border of the species range, EGS currently occurs on 34 localities, which are relatively small and isolated from each other. The spread of this species to central Europe was connected with neolithic deforestation. Disjunctive type of distribution of EGS was caused by strong decline of its abundance during the second half of the 20th century due to changes in field management, fragmentation of landscape and other factors. It can be expected that this process left traces on the genetic structure of EGS populations. The major objective of this study was a detailed analysis of genetic variability of EGS populations in the Czech Republic and searching for corelations with available data about its biology and demography. It was used 13 microsatellite loci and in total were processed 408 samples from 27 localities in CZ and 3 samples from one Hungarian locality as an outgroup. With aid of various methods, details of substructure and diferentiation of individual populations, genetic variability, degree of inbreeding and geographic distribution of genetic variability...

Thesis(M. A. Agricultural Management (Animal Production)) -- University of Limpopo, 2019 / The study was conducted to assess phenotypic and genotypic diversity in resistance to gastro-intestinal nematode (GIN) within communal goats in different agro-ecological zones of Limpopo province. Eighty goats were randomly sampled from Mopani = 20, Blouburg = 20, Vhembe = 20 and Capricorn = 20, representing four agro-ecological zones of Limpopo province. Frequencies and percentages of occurrence of qualitative traits and least square means (LSM) of quantitative traits were computed. Goats were characterized as multi-coloured (67.7%), black dominant coat colour (40%), flat face profile (73.8%), erect ears (68.75%), slopping rump (47.5%), no toggles (83.8%), horned (86.3%), while 71.0% and 59.4% were straight shaped and orientated backward respectively, in all agro-ecological zones. Faecal and blood samples were collected to assess the prevalence of GIN and genetic diversity of goats. The highest prevalence and abundance GIN parasites were Haemonchus contortus (nematode = 357.42) followed by Fasciola hapatica (trematode = 163) and Moniezia (cestodes = 121.50). The patterns of GIN prevalence varied (P < 0.05) across agro-ecological zones and seasons. Prevalence of Moniezia nematode varied (P < 0.05) amongst goat sexes, whilst prevalence of other GIN’s did not vary (P>0.05). For genetic variation in GIN resistance, goats were genotyped at 15 microsatellite markers recommended by the International Society of Animal Genetics. Expected heterozygosity (HE) ranged from 0.69 in arid zone goat population to 0.76 in sub-humid zone goat population, while the observed heterozygosity (HO) ranged from 0.53 in arid zone goat population to 0.60 in sub-humid zone goat population. Mean number of alleles (MNA) per population ranged from 6.13 to 7.40. Gene differentiation (FST) among populations was low (3.6%). The results revealed that genetic relationships between populations do not reflect their geographical proximity as revealed by the Nei’s genetic distance results. Low heterozygosity resulted in reducing some fitness traits for GIN parasite resistance. Inbreed goats showed low internal parasite resistance across all agro-ecological zones.

Genetic changes likely occur in wild fish populations as a consequence of interactions with cultured fish, but to what extent do those changes threaten the maintenance of natural genetic diversity and population viability? Following a review and categorization of numerous processes suspected of being agents of post-release genetic change in recipient wild populations (Chapter 1), I focus on risks relating to the magnitude and duration of releases -- but with a twist. That is, I assume that the mean fitness of released, cultured individuals does not differ from that of the recipient natural population. Throughout, attention is devoted to potential post-release changes in inbreeding (NeI) and variance (NeV) effective population sizes -- indicators of expected rates of population-level change in inbreeding and drift variance, respectively. The reductive effect that large-scale releases exert on NeI in recipient populations can be significant. The effect is shown to be a threshold process (Chapter 2) and thus suggestive of an approach for determining risk-adverse stocking (or release) rates. This approach is utilized in Chapter 3, which describes genetic recommendations for an incipient marine stocking program. Several discordant contemporary NeI models are examined mathematically and by computer simulation (Chapter 4). I show that certain published results pertaining to the effect of multiple paternity on NeI are erroneous; a general model is described which accounts for inbreeding and relatedness in and among parents. That model is utilized in an empirical study of gene correlation in a hatchery cohort (Chapter 5). Propagation-related causes of reductions in NeI are also investigated in this cohort. Finally, extending mutational meltdown theory to accommodate fluctuating population sizes and recessive selective effects, I show that when large reductions in NeV occur (such as those that accompany admixtures of cultured and wild fish), the expected time to population inviability is significantly reduced (Chapter 6). Although a more comprehensive theoretical approach is needed, a precautionary inference may be drawn -- aquaculture-induced reductions in Ne, even though they may be transient, can lead to adverse genetic impacts. Avoidance of Ne-reductions cannot be accomplished, in a practical sense, without considering the stocking or release rates of cultured fish.

Agricultural production among the Native American populations of the Southwest declined significantly during the twentieth century. Corn, beans and squash, the three most recognized traditional food crops, remains widespread, but knowledge regarding the traditional management of these crops was lost. The loss of traditional knowledge for Southwest Indigenous Nations was more pronounced for the Southwest peach (Prunus persica) and Navajo spinach (Cleome serrulata Pursh). The Navajo, Hopi, and Zuni Nations are all seeking to increase the availability of traditional crops for their original uses, such as for food and wool dye. In order to revitalize traditional agriculture for these tribes, information regarding these crops was gathered, including: variety characterization, the horticultural basis for traditional management practices, and cultural uses and significance. Southwest peach orchards were located for seed and plant material collections to characterize their genotype and relate them to modern peach cultivars. Traditional farmers were interviewed on management practices and irrigation strategies to correlate to dendrochronology (tree-ring analysis) techniques. Dendrochronology samples included tree stumps or cores to evaluate ring growth variability, age, and life span of the orchard trees. Navajo spinach seed was collected from Chinle, Arizona for germination studies on overcoming seed dormancy. Information on both Southwest peach and Navajo spinach will be useful to encourage culturally important traditional crop management.

The study of human relatedness has long interested the population geneticist. One technique for the estimation of population relatedness is the use of isonymy analysis. The isonymy inbreeding coefficient is analogous to Wright's inbreeding coefficient F. Isonomy analysis can yield comparable results to population studies done by other means such as pedigree analysis, serological studies, and anthropometric analysis. The data used for this study was obtained from marriage records and telephone directories. Same last name marriages were observed for legitimacy and recorded when verified. A pool of last names were drawn from the marriage records. This list was used to compare and tally like names found in telephone directories for corresponding years and localities.

This thesis includes two studies: The first examined patterns of neutral genetic diversity within Bromus tectorum L. across the IMW region, and uses patterns of microsatellite (SSR) genotype distribution to make inferences about the respective roles of adaptively significant genetic variation, adaptive phenotypic plasticity, and facultative outcrossing in the ongoing invasion and recent range expansion of B. tectorum. It has been previously demonstrated that, due to extremely low outcrossing rates, it is possible to characterize individual genotypes of this species using four SSR loci. We sampled 20 individuals from each of 96 B. tectorum populations (classified by region and habitat) from throughout the IMW and used these SSR markers to characterize each individual. We found 131 four-locus SSR genotypes; however, the 14 most common genotypes collectively accounted for 79.2% of the individuals sampled. Individuals with certain SSR genotypes sorted strongly into warm or salt desert habitats (stringent habitats) and flowered earlier than individuals with genotypes from more mesic habitats, providing evidence of adaptively significant genetic variation associated with these genotypes. Other SSR genotypes were found across a wide range of habitats though they tended to be less prevalent in stringent habitats, providing evidence that adaptive phenotypic plasticity may be important for the distribution of some common genotypes. We observed very few heterozygous individuals, consistent with the highly inbreeding reproductive strategy of B. tectorum. Because specialist genotypes dominating recently invaded areas within the IMW region contained unique alleles, they are not likely to have resulted from recombination, leading us to doubt the role of facultative outcrossing as a significant mechanism facilitating the current range expansion of B. tectorum in the IMW.Previous research investigating the population and ecological genetics of Bromus tectorum L. in the North American invaded range has relied on either allozyme or microsatellite (SSR) genetic analyses, both of which have proven to have shortcomings. In order to overcome the issues associated with these other marker types, in the second study of this thesis we developed single nucleotide polymorphism (SNP) markers for B. tectorum by 1) obtaining normalized cDNA, 2) sequencing normalized cDNA using 454 sequencing, 3) aligning resultant contigs and looking for SNPs, 4) designing assays for SNP validation and genotyping using KASPar, 5) converting working KASPar assays for use with the Fluidigm EP1 platform using the 96.96 Dynamic ArrayTM IFC. Sequencing resulted in 1258041 reads, which assembled into 65486 contigs (20782 large contigs exceeding 500 base pairs). Using selection criteria of at least 10x coverage and 30% of the minor allele, 3333 putative SNPs were identified. We developed KASP assays for 255 putative SNPs, which resulted in 101 working polymorphic assays. Ninety-six assays were then successfully converted for use with KASP on the Fluidigm EP1 genotyping platform using 96.96 dynamic arrays.