Inbreeding levels in Northeast Brazil: strategies for the prospecting of new genetic disorders

A new autosomal recessive genetic condition, the SPOAN syndrome (an acronym for spastic paraplegia, optic atrophy and neuropathy syndrome), was recently discovered in an isolated region of the State of Rio Grande do Norte in Northeast Brazil, in a population that was identified by the IBGE (Brazilian Institute of Geography and Statistics) as belonging to the Brazilian communities with the highest rates of "deficiencies" (Neri, 2003), a term used to describe diseases, malformations, and handicaps in general. This prompted us to conduct a study of consanguinity levels in five of its municipal districts by directly interviewing their inhabitants. Information on 7,639 couples (corresponding to about 40% of the whole population of the studied districts) was obtained. The research disclosed the existence of very high frequencies of consanguineous marriages, which varied from about 9% to 32%, suggesting the presence of a direct association between genetic diseases such as the SPOAN syndrome, genetic drift and inbreeding levels. This fact calls for the introduction of educational programs for the local populations, as well as for further studies aiming to identify and characterize other genetic conditions. Epidemiological strategies developed to collect inbreeding data, with the collaboration of health systems available in the region, might be very successful in the prospecting of genetic disorders.

Alternative reproductive tactics, sexual selection and the effects of inbreeding in the ant Hypoponera opacior

Inbreeding can lead to a fitness reduction due to the unmasking of deleterious recessive alleles and the loss of heterosis. Therefore, most sexually reproducing organisms avoid inbreeding, often by disperal. Besides the avoidance of inbreeding, dispersal lowers intraspecific competition on a local scale and leads to a spreading of genotypes into new habitats. In social insects, winged reproductives disperse and mate during nuptial flights. Therafter, queens independently found a new colony. However, some species also produce wingless sexuals as an alternative reproductive tactic. Wingless sexuals mate within or close to their colony and queens either stay in the nest or they found a new colony by budding. During this dependent colony foundation, wingless queens are accompanied by a fraction of nestmate workers. The production of wingless reproductives therefore circumvents the risks associated with dispersal and independent colony foundation. However, the absence of dispersal can lead to inbreeding and local competition.rnIn my PhD-project, I investigated the mating biology of Hypoponera opacior, an ant that produces winged and wingless reproductives in a population in Arizona. Besides the investigation of the annual reproductive cycle, I particularly focused on the consequences of wingless reproduction. An analysis of sex ratios in wingless sexuals should reveal the relative importance of local resource competition among queens (that mainly compete for the help of workers) and local mate competition among males. Further, sexual selection was expected to act on wingless males that were previously found to mate with and mate-guard pupal queens in response to local mate competition. We studied whether males are able to adapt their mating behaviour to the current competitive situation in the nest and which traits are under selection in this mating situation. Last, we investigated the extent and effects of inbreeding. As the species appeared to produce non-dispersive males and queens quite frequently, we assumed to find no or only weak negative effects of inbreeding and potentially mechanisms that moderate inbreeding levels despite frequent nest-matings.rnWe found that winged and wingless males and queens are produced during two separate seasons of the year. Winged sexuals emerge in early summer and conduct nuptial flights in July, when climate conditions due to frequent rainfalls lower the risks of dispersal and independent colony foundation. In fall, wingless sexuals are produced that reproduce within the colonies leading to an expansion on the local scale. The absence of dispersal during this second reproductive season resulted in a local genetic population viscosity and high levels of inbreeding within the colonies. Male-biased sex ratios in fall indicated a greater importance of local resource competition among queens than local mate competition among males. Males were observed to adjust mate-guarding durations to the competitive situation (i.e. the number of competing males and pupae) in the nest, an adaptation that helps maximising their reproductive success. Further, sexual selection was found to act on the timing of emergence as well as on body size in these males, i.e. earlier emerging and larger males show a higher mating success. Genetic analyses revealed that wingless males do not actively avoid inbreeding by choosing less related queens as mating partners. Further, we detected diploid males, a male type that is produced instead of diploid females if close relatives mate. In contrast to many other Hymenopteran species, diploid males were here viable and able to sire sterile triploid offspring. They did not differ in lifespan, body size and mating success from “normal” haploid males. Hence, diploid male production in H. opacior is less costly than in other social Hymenopteran species. No evidence of inbreeding depression was found on the colony level but more inbred colonies invested more resources into the production of sexuals. This effect was more pronounced in the dispersive summer generation. The increased investment in outbreeding sexuals can be regarded as an active strategy to moderate the extent and effects of inbreeding. rnIn summary, my thesis describes an ant species that has evolved alternative reproductive tactics as an adaptation to seasonal environmental variations. Hereby, the species is able to maintain its adaptive mating system without suffering from negative effects due to the absence of dispersal flights in fall.rn

Fitness and the level of homozygosity in a social insect.

To date very few studies have addressed the effects of inbreeding in social Hymenoptera, perhaps because the costs of inbreeding are generally considered marginal owing to male haploidy whereby recessive deleterious alleles are strongly exposed to selection in males. Here, we present one of the first studies on the effects of queen and worker homozygosity on colony performance. In a wild population of the ant Formica exsecta, the relative investment of single-queen colonies in sexual production decreased with increased worker homozygosity. This may either stem from increased homozygosity decreasing the likelihood of diploid brood to develop into queens or a lower efficiency of more homozygous workers at feeding larvae and thus a lower proportion of the female brood developing into queens. There was also a significant negative association between colony age and the level of queen but not worker homozygosity. This association may stem from inbreeding affecting queen lifespan and/or their fecundity, and thus colony survival. However, there was no association between queen homozygosity and colony size, suggesting that inbreeding affects colony survival as a result of inbred queens having a shorter lifespan rather than a lower fecundity. Finally, there was no significant association between either worker or queen homozygosity and the probability of successful colony founding, colony size and colony productivity, the three other traits studied. Overall, these results indicate that inbreeding depression may have important effects on colony fitness by affecting both the parental (queen) and offspring (worker)generations cohabiting within an ant colony.

Within- and among-population impact of genetic erosion on adult fitness-related traits in the European tree frog Hyla arborea.

Assessing in wild populations how fitness is impacted by inbreeding and genetic drift is a major goal for conservation biology. An approach to measure the detrimental effects of inbreeding on fitness is to estimate correlations between molecular variation and phenotypic performances within and among populations. Our study investigated the effect of individual multilocus heterozygosity on body size, body condition and reproductive investment of males (that is, chorus attendance) and females (that is, clutch mass and egg size) in both small fragmented and large non-fragmented populations of European tree frog (Hyla arborea). Because adult size and/or condition and reproductive investment are usually related, genetic erosion may have detrimental effects directly on reproductive investment, and also on individual body size and condition that in turn may affect reproductive investment. We confirmed that the reproductive investment was highly size-dependent for both sexes. Larger females invested more in offspring production, and larger males attended the chorus in the pond more often. Our results did not provide evidence for a decline in body size, condition and reproductive effort with decreased multilocus heterozygosity both within and among populations. We showed that the lack of heterozygosity-fitness correlations within populations probably resulted from low inbreeding levels (inferior to ca. 20% full-sib mating rate), even in the small fragmented populations. The detrimental effects of fixation load were either low in adults or hidden by environmental variation among populations. These findings will be useful to design specific management actions to improve population persistence.

Milk protein polymorphisms in Brazilian Zebu cattle

Five bovine milk protein polymorphisms were studied in Zebuine cattle raised in Brazil, through horizontal electrophoresis on starch gel containing urea and 2-mercaptoethanol, using basic and acidic buffer systems. Allelic frequencies for a-La, b-Lg, aS1-Cn, b-Cn and k-Cn loci were estimated in six Gyr herds (N = 283), six Guzerat herds (N = 205), one Nelore herd (N = 17) and one Sindi herd (N = 22), all from São Paulo or Minas Gerais State, Brazil. Genotypic frequencies observed for each locus and breed studied are in accordance with the assumption of genetic equilibrium, demonstrating absence of high inbreeding levels for the breeds tested. The FST value found indicated significant genetic differentiation among breeds; however, the Gyr and Guzerat herds showed significantly different gene frequencies. Genetic distance estimates among zebuine breeds studied and the Holstein breed, taken as a reference for a taurine breed, showed strong differences between these two racial groups

Le peuplement fondateur de la région de Lotbinière et ses conséquences démogénétiques

Un effet fondateur survient lorsqu’un petit nombre d’immigrants forment une nouvelle population et qu’ainsi les descendants ont une majorité de gènes provenant de ces quelques ancêtres. L’effet fondateur québécois, qui résulte de l’établissement de quelques milliers d’immigrants français aux XVIIe et XVIIIe siècles, est bien documenté. Mais des effets fondateurs régionaux ont aussi été identifiés. Ce mémoire de maîtrise vise à déterminer si un effet fondateur régional est à l’oeuvre dans la région de Lotbinière (Chaudière-Appalaches), dont le peuplement initial remonte à la fin du XVIIe siècle. Le fichier BALSAC et le Registre de la population du Québec ancien ont permis de constituer deux groupes de descendants, 715 individus mariés à la fin du XVIIIe siècle, et 60 autres mariés à la fin du XXe siècle. Par généalogies ascendantes et descendantes, les fondateurs immigrants et régionaux de la région ont par la suite été identifiés. Les résultats indiquent que l’effet fondateur régional avait encore une forte empreinte chez le groupe de descendants du XVIIIe siècle, mais que l’impact s’atténue en ce qui concerne les descendants contemporains. L’homogénéité démontrée par les coefficients d’apparentement et l’indice de contribution génétique uniforme, le petit nombre de fondateurs régionaux et le fait que 65 % des gènes contemporains étaient déjà introduits en 1800 sont des signes qui pointent vers un effet fondateur régional. Par contre, le nonisolement de la région, la proportion modérée de gènes contemporains introduits par les premiers fondateurs régionaux et les niveaux de consanguinité semblables aux autres régions du centre du Québec, incitent à nuancer cette conclusion. En fait, il y a possiblement deux Lotbinière : le Lotbinière ancien, sur la rive et le Lotbinière nouveau, dans les terres; chacun ayant son pool génique et son historique de peuplement propre.

Selection strategies for dairy buffaloes: economic and genetic consequences

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo hierárquico do sistema de reprodução entre e dentro de frutos, fluxo de pólen e estrutura genética espacial em um fragmento e em árvores isoladas na pastagem de hymenaea stigonocarpa mart. ex hayne na região de cerrado

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Heterosis in maize (Zea mays, L.): characterization of heterotic quantitative trait loci (QTL) for agronomic traits in near isogenic lines (NILs) and their testcrosses

In a previous study on maize (Zea mays, L.) several quantitative trait loci (QTL) showing high dominance-additive ratio for agronomic traits were identified in a population of recombinant inbred lines derived from B73 × H99. For four of these mapped QTL, namely 3.05, 4.10, 7.03 and 10.03 according to their chromosome and bin position, families of near-isogenic lines (NILs) were developed, i.e., couples of homozygous lines nearly identical except for the QTL region that is homozygote either for the allele provided by B73 or by H99. For two of these QTL (3.05 and 4.10) the NILs families were produced in two different genetic backgrounds. The present research was conducted in order to: (i) characterize these QTL by estimating additive and dominance effects; (ii) investigate if these effects can be affected by genetic background, inbreeding level and environmental growing conditions (low vs. high plant density). The six NILs’ families were tested across three years and in three Experiments at different inbreeding levels as NILs per se and their reciprocal crosses (Experiment 1), NILs crossed to related inbreds B73 and H99 (Experiment 2) and NILs crossed to four unrelated inbreds (Experiment 3). Experiment 2 was conducted at two plant densities (4.5 and 9.0 plants m-2). Results of Experiments 1 and 2 confirmed previous findings as to QTL effects, with dominance-additive ratio superior to 1 for several traits, especially for grain yield per plant and its component traits; as a tendency, dominance effects were more pronounced in Experiment 1. The QTL effects were also confirmed in Experiment 3. The interactions involving QTL effects, families and plant density were generally negligible, suggesting a certain stability of the QTL. Results emphasize the importance of dominance effects for these QTL, suggesting that they might deserve further studies, using NILs’ families and their crosses as base materials.

Deriva genética de caracteres quantitativos em milho

A obtenção de genótipos superiores no melhoramento de plantas depende da existência de variabilidade genética. A existência de coleções de germoplasma representativas e a utilização de um tamanho adequado de amostra são fundamentais para a preservação das frequências alélicas e genotípicas, diminuindo a perda de variabilidade genética e postergando o aparecimento dos efeitos da deriva genética. Assim, teve-se como objetivo avaliar os efeitos da deriva genética em caracteres quantitativos em subpopulações de milho. Este estudo foi realizado a partir das populações originais BR-105 e BR-106, das quais 10 subpopulações foram obtidas em cada um dos cinco ciclos sucessivos de amostragem com tamanho efetivo reduzido, totalizando 50 subpopulações para cada população original, as quais foram posteriormente autofecundadas, gerando um nível a mais de endogamia. Os tratamentos foram constituídos de 10 amostras da população original sem autofecundação, 10 amostras com autofecundação, 50 subpopulações obtidas da população original e 50 subpopulações autofecundadas, totalizando 120 tratamentos para cada população, avaliados separadamente. Utilizou-se o delineamento em blocos casualizados no esquema de parcelas subdivididas em faixas hierárquico, em quatro ambientes com duas repetições por ambiente. Os caracteres avaliados foram produção de grãos (PG), prolificidade (PROL), comprimento e diâmetro de espigas (CE e DE), número de fileiras por espiga (NFE), número de grãos por fileira (NGF), altura de planta e espiga (AP e AE), florescimento masculino e feminino (FM e FF) e número de ramificações do pendão (NRP). Foram estimados os efeitos da deriva genética entre as médias das subpopulações nos dois níveis de endogamia e os efeitos da depressão por endogamia nas subpopulações dentro dos ciclos. Posteriormente, realizaram-se análises de regressão linear para as subpopulações nos dois níveis de endogamia, separadamente, e em conjunto. Foi verificada uma grande variação nas médias das subpopulações ao longo dos ciclos, indicando que a deriva genética causou diferenciação entre as mesmas e que estas se diferenciaram das populações originais. Detectaram-se efeitos significativos da deriva genética nas populações não autofecundadas para todos os caracteres avaliados, em maior número para PG, já que este caráter é mais sensível à deriva genética por possuir maior grau de dominância que os demais. Houve diminuição no número de estimativas de deriva significativas para as populações autofecundadas, incluindo mudanças na magnitude e no sinal das mesmas em relação às populações não autofecundadas. Para as estimativas de depressão por endogamia, os caracteres PG, NGF, FM e FF apresentaram maior quantidade de estimativas significativas que os demais. Para a maioria dos caracteres, a regressão linear explicou a maior parte da variação encontrada com o aumento dos coeficientes de endogamia. As populações BR-105 e BR-106, por terem estruturas genéticas distintas, apresentaram performances diferentes quanto aos efeitos da deriva genética. Enfim, como a deriva genética interfere na integridade genética das populações, torna-se importante considerar seus efeitos na coleta e manutenção dos bancos de germoplasma e nas populações utilizadas no melhoramento genético de plantas.

GENETIC VARIATION, LOCAL ADAPTATION AND POPULATION STRUCTURE IN NORTH AMERICAN RED OAK SPECIES, QUERCUS RUBRA L. AND Q. ELLIPSOIDALIS E. J. HILL

Forest trees, like oaks, rely on high levels of genetic variation to adapt to varying environmental conditions. Thus, genetic variation and its distribution are important for the long-term survival and adaptability of oak populations. Climate change is projected to lead to increased drought and fire events as well as a northward migration of tree species, including oaks. Additionally, decline in oak regeneration has become increasingly concerning since it may lead to decreased gene flow and increased inbreeding levels. This will in turn lead to lowered levels of genetic diversity, negatively affecting the growth and survival of populations. At the same time, populations at the species’ distribution edge, like those in this study, could possess important stores of genetic diversity and adaptive potential, while also being vulnerable to climatic or anthropogenic changes. A survey of the level and distribution of genetic variation and identification of potentially adaptive genes is needed since adaptive genetic variation is essential for their long-term survival. Oaks possess a remarkable characteristic in that they maintain their species identity and specific environmental adaptations despite their propensity to hybridize. Thus, in the face of interspecific gene flow, some areas of the genome remain differentiated due to selection. This characteristic allows the study of local environmental adaptation through genetic variation analyses. Furthermore, using genic markers with known putative functions makes it possible to link those differentiated markers to potential adaptive traits (e.g., flowering time, drought stress tolerance). Demographic processes like gene flow and genetic drift also play an important role in how genes (including adaptive genes) are maintained or spread. These processes are influenced by disturbances, both natural and anthropogenic. An examination of how genetic variation is geographically distributed can display how these genetic processes and geographical disturbances influence genetic variation patterns. For example, the spatial clustering of closely related trees could promote inbreeding with associated negative effects (inbreeding depression), if gene flow is limited. In turn this can have negative consequences for a species’ ability to adapt to changing environmental conditions. In contrast, interspecific hybridization may also allow the transfer of genes between species that increase their adaptive potential in a changing environment. I have studied the ecologically divergent, interfertile red oaks, Quercus rubra and Q. ellipsoidalis, to identify genes with potential roles in adaptation to abiotic stress through traits such as drought tolerance and flowering time, and to assess the level and distribution of genetic variation. I found evidence for moderate gene flow between the two species and low interspecific genetic differences at most genetic markers (Lind and Gailing 2013). However, the screening of genic markers with potential roles in phenology and drought tolerance led to the identification of a CONSTANS-like (COL) gene, a candidate gene for flowering time and growth. This marker, located in the coding region of the gene, was highly differentiated between the two species in multiple geographical areas, despite interspecific gene flow, and may play a role in reproductive isolation and adaptive divergence between the two species (Lind-Riehl et al. 2014). Since climate change could result in a northward migration of trees species like oaks, this gene could be important in maintaining species identity despite increased contact zones between species (e.g., increased gene flow). Finally I examined differences in spatial genetic structure (SGS) and genetic variation between species and populations subjected to different management strategies and natural disturbances. Diverse management activities combined with various natural disturbances as well as species specific life history traits influenced SGS patterns and inbreeding levels (Lind-Riehl and Gailing submitted).

A Pollen Chase Experiment; Examining Varying Levels of Embryonic Inbreeding Depression

A pollen chase experiment was performed upon three Costa Rican populations of Witheringia solanacea to examine the breakdown of genetically enforced self incompatibility (SI) and the extent of embryonic inbreeding depression. Self-pollen was applied in the bud, with outcross pollen applied one day later, and outcross pollinations at both intervals as a control. A variety of responses were found among the populations. BOHS readily accepted self pollen and suffered from very low inbreeding depression. Monteverde and Las Cruces both have lower fruit set with self-pollination precedence indicating that bud pollinations can overcome the self-incompatibility response and that embryonic death due to inbreeding depression causes fruit failure. The treatment:control fruit set is higher for the Las Cruces plants indicating stronger SI response Self-precedence seeds from the Las Cruces plants are likely to be outcrossed. Self-precedence seeds from Monteverde are likely selfed.

What the reasons for no inbreeding and high genetic diversity of the neotropical fig tree Ficus arpazusa ?

Ficus arpazusa Casaretto is a fig tree native to the Atlantic Rain Forest sensu lato. High levels of genetic diversity and no inbreeding were observed in Ficus arpazusa. This genetic pattern is due to the action of its pollinator, Pegoscapus sp., which disperses pollen an estimated distance of 5.6 km, and of Ficus arpazusa`s mating system which, in the study area, is allogamous. This study highlights the importance of adding both ecological and genetic data into population studies, allowing a better understanding of evolutionary processes and in turn increasing the efficacy of forest management and revegetation projects, as well as species conservation.

Variable queen number in ant colonies: no impact on queen turnover, inbreeding, and population genetic differentiation in the ant Formica selysi.

Variation in queen number alters the genetic structure of social insect colonies, which in turn affects patterns of kin-selected conflict and cooperation. Theory suggests that shifts from single- to multiple-queen colonies are often associated with other changes in the breeding system, such as higher queen turnover, more local mating, and restricted dispersal. These changes may restrict gene flow between the two types of colonies and it has been suggested that this might ultimately lead to sympatric speciation. We performed a detailed microsatellite analysis of a large population of the ant Formica selysi, which revealed extensive variation in social structure, with 71 colonies headed by a single queen and 41 by multiple queens. This polymorphism in social structure appeared stable over time, since little change in the number of queens per colony was detected over a five-year period. Apart from queen number, single- and multiple-queen colonies had very similar breeding systems. Queen turnover was absent or very low in both types of colonies. Single- and multiple-queen colonies exhibited very small but significant levels of inbreeding, which indicates a slight deviation from random mating at a local scale and suggests that a small proportion of queens mate with related males. For both types of colonies, there was very little genetic structuring above the level of the nest, with no sign of isolation by distance. These similarities in the breeding systems were associated with a complete lack of genetic differentiation between single- and multiple-queen colonies, which provides no support for the hypothesis that change in queen number leads to restricted gene flow between social forms. Overall, this study suggests that the higher rates of queen turnover, local mating, and population structuring that are often associated with multiple-queen colonies do not appear when single- and multiple-queen colonies still coexist within the same population, but build up over time in populations consisting mostly of multiple-queen colonies.

Inbreeding and selection on sex ratio in the bark beetle Xylosandrus germanus.

ABSTRACT: BACKGROUND: Local Mate Competition (LMC) theory predicts a female should produce a more female-biased sex ratio if her sons compete with each other for mates. Because it provides quantitative predictions that can be experimentally tested, LMC is a textbook example of the predictive power of evolutionary theory. A limitation of many earlier studies in the field is that the population structure and mating system of the studied species are often estimated only indirectly. Here we use microsatellites to characterize the levels of inbreeding of the bark beetle Xylosandrus germanus, a species where the level of LMC is expected to be high. RESULTS: For three populations studied, genetic variation for our genetic markers was very low, indicative of an extremely high level of inbreeding (FIS = 0.88). There was also strong linkage disequilibrium between microsatellite loci and a very strong genetic differentiation between populations. The data suggest that matings among non-siblings are very rare (3%), although sex ratios from X. germanus in both the field and the laboratory have suggested more matings between non-sibs, and so less intense LMC. CONCLUSIONS: Our results confirm that caution is needed when inferring mating systems from sex ratio data, especially when a lack of biological detail means the use of overly simple forms of the model of interest.