Although the process by which fertilization occurs in bryozoans is well described, the ability to self-fertilize and the subsequent ecological consequences are poorly understood. Culturing experiments were conducted examining the effects of selfing on offspring survival and reproduction in the simultaneous hermaphrodite Bugula stolonifera collected from Eel Pond, Woods Hole, MA. Results from these experiments document significant decreases in survival and fecundity of selfed offspring, compared to outcrossed controls, suggesting that these animals are not routinely self-fertilizing in Eel Pond. How these arborescent colonies minimize selfing remains unclear, but it is hypothesized that conspecific aggregations could serve to minimize the chances that a colony utilizes its own sperm for fertilization. The genetic composition of these aggregations was investigated using a newly developed microsatellite library. As larvae routinely metamorphose on conspecific colonies, the possibility that larvae select or avoid their maternal colony was also investigated. Analyses of genetic structure document homogeneity throughout these aggregations on extremely small spatial scales, suggesting high amounts of larval dispersal within aggregations. When combined with results from parentage-exclusion and kinship analyses, these results indicate that a colony's nearest neighbors are not composed of siblings, potentially minimizing inbreeding. Molecular analyses were then used to determine if the high larval dispersal within aggregations resulted in high mixing between aggregations. Sites within Eel Pond separated by 100-300 m were routinely sampled from 2009 to 2011, and analyses were conducted to investigate potential inter- and intra-annual genotypic differentiation within and between aggregations. Results document that although low levels of mixing could result in increased homogeneity between some aggregations, barriers to genetic exchange prevent mixing between most sites. Further, inter-annual comparisons within sites document that significant differentiation can occur between reproductive seasons. Hence, any potential homogeneity achieved between sites during one reproductive season will likely be lost by the beginning of the next reproductive season. Additionally, while sampling in Eel Pond in 2010, I document the first occurrence from the western Atlantic Ocean of another aggregating arborescent bryozoan, Tricellaria inopinata. The growth and reproductive biology of these animals was monitored throughout 2011; results suggest that this introduction is likely to persist.

This thesis gives a genetic overview of the Hays Converter, a beef breed developed in Canada in the 1950s. Pedigree records were examined to determine genetic diversity and inbreeding. A positive rate of inbreeding and a decrease in the amount of genetic diversity was found. Single trait and bivariate animal models were used to determine genetic parameters and trends for growth, ultrasound, and carcass traits. An increasing genetic trend was found for growth traits which the breed was selected for. The accuracy of imputation from 6k to 50k marker panels using a reference group of 100 animals was determined. Imputation was performed with a high accuracy (>0.93) for pure Hays Converter animals, but was found to be unsuccessful when individuals had large contributions from additional breeds. This work forms the foundation for future management and advance of the breed while outlining its history and progress. / Daniel P. Hays

It is generally accepted that populations which experience severe bottlenecks have a reduction in fitness. One of the most frequently reported fitness costs is increased hatching failure in bottlenecked populations of birds. The mechanism responsible for increased hatching failure is unknown. Research on other animals suggest that reduced population numbers cause unavoidable inbreeding that in turn leads to abnormalities in the gametes. In this thesis I examine some of the possible causes for increased hatching failure in severely bottlenecked populations of introduced birds in New Zealand. I look at three traits identified as a cause for infertility or hatching failure previously and determine whether there is a link with the size of a population s bottleneck. It is possible that reduced numbers of sperm reaching the site of fertilisation is a primary cause of hatching failure. I examined the perivitelline membrane of various species of introduced birds and counted the total number of sperm present to compare to how many would be expected in non-bottlenecked species. Although there was no relationship between the size of the bottleneck and the number of sperm present, all species had lower than expected sperm counts. In many species of mammals, a reduction in the quality of sperm is attributed to inbreeding depression bought about by genetic bottlenecks. I next compared the level of sperm abnormalities, variation in midpiece size sperm, and sperm motility with the size of the bottleneck each species passed through when introduced to New Zealand. There was no significant correlation between either the variation in midpiece size or sperm motility with bottleneck size. However, there was a trend for species that passed through more severe bottlenecks to have a slightly higher level of midpiece size and lower motility. Finally, I examined whether there was a link between abnormalities in the eggshell and the size of the respective bottleneck. There was no significant change in eggshell thickness or any change in the number of pores associated bottleneck size. However, there was a decreased number of round pores in severely bottlenecked species, although the consequences of this are unknown. My findings do not directly link a single cause for increased hatching failure in bottlenecked species of birds, but they do highlight the need for monitoring of reproductive traits in endangered species that have experienced a population bottleneck.

Thesis(M.S.)--Auburn University, 2005. / Abstract. Vita. Includes bibliographic references.

Thesis (Ph. D.)--University of Missouri-Columbia, 1997. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 1997. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

Orientador: Danísio Prado Munari / Coorientador: Marcos Eli Buzanskas / Coorientador: Mônica Corrêa Ledur / Coorientador: Rodrigo Pelicioni Savegnago / Banca: Claudia Cristina Paro de Paz / Banca: Nedenia Bonvino Stafuzza / Resumo: Galinhas são responsáveis por significativa parcela da produção de proteína para o consumo humano no mundo, movimentando a economia de diversos países. Com desenvolvimento de tecnologias de genotipagem de polimorfismos com painéis de alta densidade tornou-se possível a realização de estudos de associação ampla do genoma (GWAS) com características de importância econômica para a indústria avícola e também sua incorporação como ferramenta em estudos de conservação genética e de estrutura populacional em frangos de corte. No presente estudo objetivou-se avaliar a estrutura populacional de uma linhagem de frangos de corte por meio da análise conjunta de informações do desequilíbrio de ligação (DL), tamanho efetivo populacional (Ne), coeficiente de endogamia e segmentos de homozigose (ROH) e realizar GWAS com características de eficiência alimentar e crescimento. Para isso foram utilizadas 1.433 aves provenientes da expansão de uma linha paterna de frangos de corte genotipadas com o painel 600K Affymetrix® Axiom® HD (Affymetrix®). No controle de qualidade, foram excluídos SNPs com "call rate" abaixo de 98%, desvio do equilíbrio de Hardy-Weinberg (p-valor ≤ 10-6) e cuja frequência do alelo raro foi inferior a 2%, utilizando-se apenas os cromossomos GGA1 ao GGA28 para o estudo da estrutura populacional. Para o estudo de GWAS foram utilizados os cromossomos autossômicos e grupos de ligação (programas SNP1101 e QxPak) e cromossomo sexual Z (programa QxPak). O control... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Chickens are responsible for a significant portion of protein production for human consumption in the world, moving the economy of many countries. The development of high-density arrays made possible the genome-wide association study (GWAS) for economic important traits to the poultry industry as well as its incorporation as a tool for genetic conservation and population structure studies in broilers. The present study aimed to evaluate the population structure of a broiler line of through the joint analysis of linkage disequilibrium (LD), effective population size (Ne), inbreeding coefficient and runs of homozygosity (ROH), and performing GWAS with growth and feed efficiency traits in a population from a male broilers line. A total of 1,433 birds were used from an expansion population of a paternal broiler line genotyped with 600K Affymetrix® Axiom® HD array (Affymetrix®). The genotype quality control considered the exclusion of single nucleotide polymorphisms (SNPs) with call rate below 98%, based on the deviations from Hardy-Weinberg equilibrium (p ≤ 1x10-6), and minor allele frequency was lower than 2%, using only Gallus gallus autosomes (GGA1 to GGA28) for the population structure study, and all autosomes, linkage groups and Z chromosome sex for GWAS. Quality control samples considered the exclusion of individuals who had SNPs call rate below 90%. The LD was calculated by Plink v.1.9 software using the correlation between two consecutive SNPs (r²). From the LD data was calculated Ne up to 200 generations ago using SNP1101 v.1.0 software. The ROH were identified using Plink v.1.9 software, which considered segments of at least 100 SNPs with a minimum length of 1,000 kb, and allowed the presence of a heterozygous SNP and the absence of one SNP in a window 100 SNPs. The GWAS analysis was performed using SNP1101 v.1.0 and QxPak 5.0 softwares ... (Complete abstract click electronic access below) / Mestre

Inbreeding was thought to be responsible for the loss in the second filial generation (F₂) of Amalafrida leithella Dyar, Cactoblastis mundelli Heinrich, Nanaia sp. Heinrich, Sigelgaita sp. Heinrich and Sigelgaita transilis Heinrich in the laboratory. This pre-empted the investigation of the effects of inbreeding on another cactophagous moth, Mimorista pulchellalis Dyar, an established biological control agent of jointed cactus in South Africa. Initially three populations were set up. A randomly-mating control (OUT 1) population, and a sibmating experimental (IN 1) population, consisted of laboratory-reared stock . A second experimental population (KR 1) comprised a small number of field-collected randomly-mating individuals which recreated the conditions under which the five abovementioned species were lost. The inbreeding depression of fifteen fitness components was assessed. The mean values of each component in each generation of treatments IN 1 and KR 1 were compared with those of OUT 1. In addition the mean values of IN 1 were regressed against the coefficients of inbreeding since inbreeding depression is linear with respect to the probability of two genes at any locus being homozygous through ancestry. The component egg viability was important because a reduction in OUT 1, IN 1 and KR 1 in the F₂ resulted from mated females producing no viable eggs. Duplicate treatments OUT 2, IN 2 and KR 2 were set up to confirm whether this was a general F₂ phenomenon. Assessment of the fitness components prevented a direct evaluation of the numbers of offspring produced. However a hypothetical estimate of population size and growth rate was made using the percentage survival calculated from life-table analysis. Although not statistically demonstrable in the component analysis, life table analysis indicated that egg viability suffered an inbreeding depression and affected population fitness. It was also evident that treatments OUT 1 and 2 were fitter than treatments IN 1 and 2 and KR 1 and 2 with respect to population fitness. Thus, inbreeding, resulting from sibmating and introduction of a small number of individuals to a laboratorYJ caused a decrease in numbers of offspring produced and population growth rate. This is important in relation to the demise of the cactophagous Lepidoptera and to future biological control programmes.

Ma thèse s’intéresse à l’influence des comportements culturels sur la diversité génétique neutre des populations humaines, en particulier les populations d’Asie intérieure. Notamment, ces travaux explorent comment certains comportements affectent l’histoire démographique des populations, en agissant sur l’intensité des migrations et de la dérive génétique. Pour ce faire, j’ai étudié des données génétiques, au regard de données ethnologiques, collectées dans des populations habitant actuellement en Asie intérieure, qui diffèrent, entre autres, par leur organisation sociale. La première partie de cette thèse cherche à retracer l’histoire du peuplement de l’Asie intérieure, de l’âge du Bronze jusqu’à nos jours à partir données génomiques d’ADN moderne et ancien. Les résultats montrent que les populations actuelles forment deux groupes génétiques distincts correspondant à deux groupes linguistiques (Turco-Mongol et Indo-Iranien) et reflétant des composantes ancestrales contrastées. En étudiant la diversité génétique de marqueurs uniparentaux, j’ai montré des différences génétiques sexe-spécifiques telles qu’une différenciation des populations réduite pour l’ADN mitochondrial par rapport à celle du chromosome Y. Cette homogénéité génétique des populations pourrait être causée par de la patrilocalité, une règle de résidence commune à toutes les populations étudiées et entrainant principalement des migrations féminines entre populations. D’autre part, j’ai observé des différences de diversité génétique entre les groupes d’Asie intérieure pour le chromosome Y, que j’ai interprété à la lumière des différences de règles de filiation suivies par ces deux groupes : l’un des groupes est patrilinéaire, c’est-à-dire que la filiation sociale est héritée du père ; l’autre groupe est cognatique, et la transmission est indifférenciée entre les parents. La patrilinéarité conduirait à la formation de noyaux d’hommes apparentés par la lignée masculine dans la population et donc partageant le même chromosome Y, ce qui réduirait la diversité génétique du chromosome Y des populations patrilinéaires, comparées aux cognatiques. La diversité mitochondriale est, par contre, similaire entre patrilinéaires et cognatiques, illustrant le fait que seule la diversité génétique masculine est affectée par la patrilinéarité. Enfin, pour étudier le processus d’ethnogénèse, j’ai calculé l’âge génétique des groupes ethniques patrilinéaires et j’ai montré que cet âge biologique est plus ancien que les âges historiques, suggérant que l’ethnie, du moins chez les Turco-Mongols d’Asie intérieure, est une construction en partie sociale, plutôt qu’une entité entièrement biologique. Dans la troisième partie, je me suis intéressée aux mécanismes d’évitement de la consanguinité, que j’ai estimée au moyen de données génomiques. J’ai notamment testé l’hypothèse selon laquelle des unions exogames, entre conjoints nés dans des villages différents, permettraient de réduire la consanguinité. Malgré une importante variabilité du taux d’exogamie entre populations et entre groupes linguistiques dans notre jeu de données, je n’ai trouvé aucune différence significative de consanguinité. A l’échelle des individus, j’ai pu mettre en évidence le fait que certains descendants de couples exogames sont néanmoins consanguins. Cette situation est particulièrement répandue pour des conjoints nés à moins de 40 km l’un de l’autre, à tel point que leurs descendants sont statistiquement plus consanguins que les descendants de couples endogames. Ces résultats illustrent que, chez l’Homme, des comportements culturels d’alliance peuvent s’opposer aux attendus de la biologie évolutive. Ainsi, mes travaux illustrent plusieurs cas de figure, à des échelles géographiques et temporelles différentes, où des comportements culturels ont modifié et laissé une signature génétique particulière sur la diversité des populations humaines d’Asie intérieure. / My PhD thesis is about the influence of cultural behaviours on the neutral genetic diversity of human populations from Inner Asia. Notably, I investigated how specific behaviours may affect the demographic history of populations, by acting on the intensity of migration and genetic drift. To do so, I combined genetic and ethnological data, collected in present-day Inner Asian populations that belong to two major cultural and linguistic groups and have different social organisations.The first part of this work aims at understanding how Inner Asia was peopled, from the Bronze Age to nowadays. This was done in the framework of an international collaboration, through the study of both ancient and modern genomic data. The results obtained showed that modern populations are divided in two distinct genetic groups, mirroring the two cultural groups, and exhibiting contrasted ancestral components. I was then interested in exploring the influence of cultural behaviours on the sex-specific genetic structure of present-day populations from Inner Asia. By studying the genetic diversity of uniparental markers, namely mitochondrial DNA and the Y chromosome, I was able to characterize sex-specific genetic differences, such as a reduced population differentiation for mitochondrial DNA as compared to the Y chromosome. This maternal genetic homogeneity between populations may be explained by patrilocality, a residence rule shared by all the studied populations and generating mostly female migrations between populations. On the other hand, I showed there were some significant differences in genetic diversity between the two cultural groups for the Y chromosome. This observation may be related to the different filiation rules of these two groups. Indeed, one is patrilineal: the social filiation is inherited from the father, while the other is cognatic: the transmission is undifferentiated between the parents. It could then be that patrilineality leads to the formation of cores of related men within the population, who share the same Y chromosome. This population structuration would result in a reduced genetic diversity for the Y chromosome in patrilineal populations, compared to cognatics. As expected, the mitochondrial diversity is comparable between patrilineal and cognatic group, comforting the idea that patrilineality affects only the male genetic diversity. Finally, to investigate the ethnogenesis process, I calculated the genetic age of patrilineal ethnic groups from STR markers of the Y chromosome. I showed that this biological age is older than the one from historical sources, which suggests that, at least for Turko-Mongolic from Inner Asia, the ethnic group is partly a social construct, rather than an actual biological entity. In the third part, I focused on whether dispersal can be an inbreeding avoidance mechanisms by dispersal. Notably, I tested the hypothesis that exogamous unions, between spouses born in different villages, would lead to less inbreeding than endogamous unions. Despite a strong variation of the exogamous rate between the populations of the studied dataset, no significant difference was found for inbreeding, which was estimated from a genome-wide dataset. At the individual scale, I showed that some of the descendants of exogamous unions are inbred. This is especially true for spouses born less than 40 km away, in which case their descendants are statistically more inbred than those from endogamous unions. This shows that, in human populations, specific matrimonial behaviours, driven by culture, may contradict the results expected by evolutionary biology.In conclusion, my work shows several cases, at different time and geographic scales, where cultural behaviours left a footprint into the genetic diversity of Inner Asian populations.

Submitted by Ricardo Faria (fariasky@gmail.com) on 2016-03-19T01:28:20Z No. of bitstreams: 1 DISSERTACAO_RICARDO_ANTONIO_DA_SILVA_FARIA.pdf: 1017582 bytes, checksum: 84a709da815cc0db9987696624f4e936 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-03-22T13:37:57Z (GMT) No. of bitstreams: 1 faria_ras_me_jabo.pdf: 1017582 bytes, checksum: 84a709da815cc0db9987696624f4e936 (MD5) / Made available in DSpace on 2016-03-22T13:37:57Z (GMT). No. of bitstreams: 1 faria_ras_me_jabo.pdf: 1017582 bytes, checksum: 84a709da815cc0db9987696624f4e936 (MD5) Previous issue date: 2016-02-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A raça Quarto de Milha (QM) teve seus primeiros exemplares criados no Brasil em 1956, cujos pais foram importados dos Estados Unidos, com fundação da associação dos criadores em 1969, totalizando mais de 415 mil animais registrados e destes 45% são puros. A raça apresenta-se como versátil para trabalho, conformação e corrida, atributos que a tornam como de escolha entre os criadores e de maior população equina nacional. Apesar disto, poucos estudos foram realizados na raça, particularmente acerca da variabilidade genética. Os objetivos do estudo foram obter informações da estrutura populacional da raça QM no Brasil e estimar os parâmetros genéticos da característica Classe de Tempo (CT), relacionada com a performance em corridas de equinos em diferentes distâncias. O escore aplicado a CT, classifica os animais baseado na comparação percentual de tempo do vencedor de cada páreo. Os dados avaliados foram provenientes da Associação Brasileira de Criadores do Cavalo Quarto de Milha e do hipódromo do Jockey Clube de Sorocaba em São Paulo. A preparação da base de dados e estatística inicial foi realizada no programa SAS, os parâmetros populacionais com o programa ENDOG e os componentes de (co) variâncias e parâmetros genéticos com o programa THRGIBBS1F90. A característica CT foi estabelecida nas corridas com distância de 301 (CT301), 320 (CT320), 365 (CT365) e 402 (CT420) metros e analisada por meio de modelo animal limiar. Os parâmetros populacionais obtidos foram 0,49% de endogamia, 0,29% de parentesco, 9,3 anos de intervalo gerações, a probabilidade de origem dos genes com valor igual a 333 de número efetivo de fundadores, a variabilidade genética total apresentou-se explicada por 7.254 ancestrais, com 161 ancestrais explicando 50%. As estimativas a posteriores da herdabilidade e da repetibilidade, obtidas em análise multicaracterística, foram de 0,52±0,04 e 0,85±0,04 (CT301), 0,48±0,06 e 0,97±0,01 (CT320), 0,56±0,04 e 0,88±0,06 (CT365) e 0,45±0,06 e 0,78±0,04 (CT420), respectivamente. Os valores obtidos indicam que a característica CT pode ser utilizada como critério de seleção e obter rápido ganho genético. A baixa variabilidade genética na raça Quarto de Milha foi evidenciada, sugerindo aos criadores inserção de reprodutores no rebanho. / The Quarter Horse (QH) had its first specimens bred in Brazil in 1956, whose parents were imported from the United States, with its breeder association founded in 1969, totaling more than 415,000 registered animals and of these 45% are purebred. The breed is versatile in what concerns performance, conformation and racing, attributes that make the QH the breed of choice among breeders and makes it the largest national equine population. In spite of that, few studies have been conducted about the breed, particularly on the genetic variability of strains. The aim of this study was to gather information about the population structure and estimate the genetic parameters of the trait class time (CT) related to performance in different QH racing distances, contributing with results that enable their use in the design of animal breeding programs aimed at maintaining the variability of the breed and decreasing race times. The score applied to CT, ranks animals based on comparing percentage winning time of each match. The analyzed data originates from the Brazilian Association of Breeders of Quarter Horse and Jockey Clube de Sorocaba’s hippodrome, in Sao Paulo. The preparation of the initial data and statistical base was done using SAS software, the population parameters with the ENDOG software and the (co) variances and genetic parameters components with the THRGIBBS1F90 software. The CT characteristic was established in racing with 301 (CT301), 320 (CT320), 365 (CT365) and 402 (CT420) meters distances and analyzed by threshold animal model. The obtained population parameters were 0.49% of inbreeding, 0.29% of kinship, 9.3-year generation interval, The probability of origin of genes with value 333 related to effective number of founders, the total genetic variability is explained by 7,254 ancestors, with 161 ancestors responsible for 50%. The estimates later heritability and repeatability obtained in multi-trait analysis were 0.52 ± 0.04 and 0.85 ± 0.04 (CT301), 0.48 ± 0.06 and 0.97 ± 0, 01 (CT320), 0.56 ± 0.04 and 0.88 ± 0.06 (CT365) and 0.45 ± 0.06 and 0.78 ± 0.04 (CT420), respectively. The values obtained indicate that CT feature can be used as selection criteria and obtain rapid genetic gain. The low genetic variability in the Quarter Horse breed was evidenced, suggesting to breeding insertion breeders in the herd.