The Pollination Biology and Mating System of a Peripheral Population of Witheringia solanacea (Solanaceae)

Pollinator visitation rates over the life of a flower are determined by pollinator abundance and floral longevity. If flowers are not visited frequently enough, pollen limitation may occur, favoring the evolution of self-compatibility (SC). In plant species with varying SC levels, central populations often are self-incompatible (SI) and peripheral populations are SC. Witheringia solanacea (Solanaceae) is a species that follows this trend with the exception of one population in the Monteverde Cloud Forest Reserve, which is peripheral yet SI. I investigated this population using multiple techniques including floral bagging, pollinator observations, microsatellite analysis, and floral longevity manipulations. My results confirmed the self-incompatibility of the Monteverde population and indicated low but perhaps adequate rates of pollinator visitation per flower per hour. I found reduced genetic diversity at Monteverde and gene flow occurring unidirectionally from San Luis (a central population) to Monteverde. In the greenhouse, there was more of an effect of male than female function on floral longevity, but the largest differences were environmental. Flowers stayed open substantially longer when cool, cloudy weather was simulated and shorter when conditions were hot and sunny. The results indicate that the Monteverde population of W. solanacea is SI because 1) it is unable to maximize its fitness due to gene flow from San Luis and its relatively recent colonization of the area and 2) pollen limitation may not be severe because of supplemental pollinator availability from other Witheringia species in the area and increased floral longevities due to cool and cloudy conditions.

Phylogeography and Pleistocene demographic history of the endangered marsh deer (Blastocerus dichotomus) from the Rio de la Plata Basin

The marsh deer is the largest neotropical cervid with morphological and ecological adaptations to wetlands and riparian habitats. Historically, this now endangered species occupied habitats along the major river basins in South America, ranging from southern Amazonia into northern Argentina to the Parana river delta. This particularly close association with wetlands makes marsh deer an excellent species for studying the effects of Pleistocene climatic changes on their demographic and phylogeographic patterns. We examined mitochondrial DNA variation in 127 marsh deer from 4 areas distributed throughout the Rio de]a Plata basin. We found 17 haplotypes in marsh deer from Brazil, Bolivia and Argentina that differed by 1-8 substitutions in a 601 bp fragment of mitochondrial control region sequence, and 486 bp of cytochrome b revealed only 3 variable sites that defined 4 haplotypes. Phylogeny and distribution of control region haplotypes suggest that populations close to the Pantanal area in central Brazil underwent a rapid population expansion and that this occurred approximately 28,000-25,000 years BP. Paleoclimatic data from this period suggests that there was a dramatic increase for precipitation in the medium latitudes in South America and these conditions may have fostered marsh deer's population growth.

Evaluation of nine microsatellite loci and misidentification paternity frequency in a population of Gyr breed bovines

Erros de identificação de paternidade são prejudiciais por reduzir o ganho genético anual e comprometer um programa eficiente de melhoramento genético. O objetivo principal deste trabalho foi avaliar o potencial de uso de nove microssatélites em testes de paternidade e investigar a freqüência de erro de identificação de famílias de um rebanho de animais da raça Gir. No experimento foram utilizadas amostras de sangue de quarenta famílias (touro/ vaca/ bezerro) de animais da raça Gir, Puros de Origem e registrados na Associação Brasileira dos Criadores de Zebu (ABCZ). A maior parte dos microssatélites avaliados neste trabalho são recomendados, para Testes de Paternidade em bovinos, pela Sociedade Internacional de Genética Animal (ISAG). As regiões microssatélites TGLA122, TGLA126, BM1824, BMS2533, SPS115, ETH3, ETH10, ETH225 e POTCHA foram amplificadas por meio da técnica de PCR. Os produtos da amplificação foram separados por eletroforese em gel de poliacrilamida desnaturante. A partir dos dados obtidos foram calculadas as freqüências alélicas, diversidade gênica, conteúdo de polimorfismo informativo e probabilidade de exclusão para cada microssatélite. Também foram calculadas as freqüências genotípicas, heterozigosidade, probabilidade de exclusão combinada e probabilidade de Paternidade nas famílias consideradas. A probabilidade de exclusão combinada para todos os microssatélites estudados foi de 0,9789. Os resultados dos testes de paternidade acusaram erro de identificação em onze das 40 famílias estudadas, ou seja, 27,5% da amostra. A probabilidade de paternidade variou entre 0,8691 e 0,9999, com valor médio de 0,9512.

Estimation of outcrossing rate in a breeding population of Eucalyptus urophylla with dominant RAPD and AFLP markers

Eucalyptus breeding is typically conducted by selection in open-pollinated progenies. As mating is controlled only on the female side of the cross, knowledge of outcrossing versus selling rates is essential for maintaining adequate levels of genetic variability for continuous gains. Outcrossing rate in an open-pollinated breeding population of Eucalyptus urophylla was estimated by two PCR-based dominant marker technologies, RAPD and AFLP, using 11 open-pollinated progeny arrays of 24 individuals. Estimated outcrossing rates indicate predominant outcrossing and suggest maintenance of adequate genetic variability within families. The multilcous outcrossing rate (t(m)) estimated from RAPD markers (0.93 +/- 0.027), although in the same range, was higher (alpha > 0.01) than the estimate based on AFLP (0.89 +/- 0.033). Both estimates were of similar magnitude to those estimated for natural populations using isozymes. The estimated Wright's fixation index was lower than expected based on t, possibly resulting from selection against selfed seedlings when sampling plants for the study. An empirical analysis suggests that 18 is the minimum number of dominant marker loci necessary to achieve robust estimates of t,. This study demonstrates the usefulness of dominant markers, both RAPD and AFLP, for estimating the outcrossing rate in breeding and natural populations of forest trees. We anticipate an increasing use of such PCR-based technologies in mating-system studies, in view of their high throughput and universality of the reagents, particularly for species where isozyme systems have not yet been optimized.

Contemporary pollen flow, mating patterns and effective population size inferred from paternity analysis in a small fragmented population of the Neotropical tree Copaifera langsdorffii Desf. (Leguminosae-Caesalpinioideae)

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

Ecological and evolutionary consequences of living in a defaunated world

Defaunation, the loss or population decline of medium and large native vertebrates represents a significant threat to the biodiversity of tropical ecosystems. Here we review the anthropogenic drivers of defaunation, provide a brief historical account of the development of this field, and analyze the types of biological consequences of this impact on the structure and functioning of tropical ecosystems. We identify how defaunation, operating at a variety of scales, from the plot to the global level, affects biological systems along a gradient of processes ranging from plant physiology (vegetative and reproductive performance) and animal behavior (movement, foraging and dietary patterns) in the immediate term; to plant population and community dynamics and structure leading to disruptions of ecosystem functioning (and thus degrading environmental services) in the short to medium term; to evolutionary changes (phenotypic changes and population genetic structure) in the long-term. We present such a synthesis as a preamble to a series of papers that provide a compilation of our current understanding of the impact and consequences of tropical defaunation. We close by identifying some of the most urgent needs and perspectives that warrant further study to improve our understanding of this field, as we confront the challenges of living in a defaunated world. © 2013 Elsevier Ltd.

Geoffroy's side-necked turtle [Phrynops geoffroanus (Schweigger, 1812), Testudines: Chelidae] as a model for evolutionary ecotoxicology: relationship between environmental contamination, conditions and genetic variability

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evaluation of area contaminated by wood treatment activities: genetic markers in the environment and in the child population

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effect of salinity on the metabolism and osmoregulation of selected ontogenetic stages of an Amazon population of Macrobrachium amazonicum shrimp (Decapoda, Palaemonidae)

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

QUANTITATIVE TRAIT LOCI FOR AGRONOMIC AND END-USE QUALITY PERFORMANCE AND THE EFFECT OF SOILBORNE WHEAT MOSAIC VIRUS IN A HARD WINTER WHEAT POPULATION IN NEBRASKA

To better understand agronomic and end-use quality in wheat (Triticum aestivum L.) we developed a population containing 154 F6:8 recombinant inbred lines (RILs) from the cross TAM107-R7/Arlin. The parental lines and RILs were phenotyped at six environments in Nebraska and differed for resistance to Wheat soilborne mosaic virus (WSBMV), morphological, agronomic, and end-use quality traits. Additionally, a 2300 cM genome-wide linkage map was created for quantitative trait loci (QTL) analysis. Based on our results across multiple environments, the best RILs could be used for cultivar improvement. The population and marker data are publicly available for interested researchers for future research. The population was used to determine the effect of WSBMV on agronomic and end-use quality and for the mapping of a resistance locus. Results from two infected environments showed that all but two agronomic traits were significantly affected by the disease. Specifically, the disease reduced grain yield by 30% of susceptible RILs and they flowered 5 d later and were 11 cm shorter. End-use quality traits were not negatively affected but flour protein content was increased in susceptible RILs. The resistance locus SbmTmr1 mapped to 27.1 cM near marker wPt-5870 on chromosome 5DL using ELISA data. Finally, we investigated how WSBMV affected QTL detection in the population. QTLs were mapped at two WSBMV infected environments, four uninfected environments, and in the resistant and susceptible RIL subpopulations in the infected environments. Fifty-two significant (LOD≥3) QTLs were mapped in RILs at uninfected environments. Many of the QTLs were pleiotropic or closely linked at 6 chromosomal regions. Forty-seven QTLs were mapped in RILs at WSBMV infected environments. Comparisons between uninfected and infected environments identified 20 common QTLs and 21 environmentally specific QTLs. Finally, 24 QTLs were determined to be affected by WSBMV by comparing the subpopulations in QTL analyses within the same environment. The comparisons were statistically validated using marker by disease interactions. These results showed that QTLs can be affected by WSBMV and careful interpretation of QTL results is needed where biotic stresses are present. Finally, beneficial QTLs not affected by WSBMV or the environment are candidates for marker-assisted selection.

Landscape ecology and genetics of the wolf in Italy

This PhD Thesis includes five main parts on diverse topics. The first two parts deal with the trophic ecology of wolves in Italy consequently to a recent increase of wild ungulates abundance. Data on wolf diet across time highlighted how wild ungulates are important food resource for wolves in Italy. Increasing wolf population, increasing numbers of wild ungulates and decreasing livestock consume are mitigating wolf-man conflicts in Italy in the near future. In the third part, non-invasive genetic sampling techniques were used to obtain genotypes and genders of about 400 wolves. Thus, wolf packs were genetically reconstructed using diverse population genetic and parentage software. Combining the results on pack structure and genetic relatedness with sampling locations, home ranges of wolf packs and dispersal patterns were identified. These results, particularly important for the conservation management of wolves in Italy, illustrated detailed information that can be retrieved from genetic identification of individuals. In the fourth part, wolf locations were combined with environmental information obtained as GIS-layers. Modern species distribution models (niche models) were applied to infer potential wolf distribution and predation risk. From the resulting distribution maps, information pastures with the highest risk of depredation were derived. This is particularly relevant as it allows identifying those areas under danger of carnivore attack on livestock. Finally, in the fifth part, habitat suitability models were combined with landscape genetic analysis. On one side landscape genetic analyses on the Italian wolves provided new information on the dynamics and connectivity of the population and, on the other side, a profound analysis of the effects that habitat suitability methods had on the parameterization of landscape genetic analyses was carried out to contributed significantly to landscape genetic theory.

Misleading Population Estimates: Biases and Consistency of Visual Surveys and Matrix Modelling in the Endangered Bearded Vulture

Conservation strategies for long-lived vertebrates require accurate estimates of parameters relative to the populations' size, numbers of non-breeding individuals (the “cryptic” fraction of the population) and the age structure. Frequently, visual survey techniques are used to make these estimates but the accuracy of these approaches is questionable, mainly because of the existence of numerous potential biases. Here we compare data on population trends and age structure in a bearded vulture (Gypaetus barbatus) population from visual surveys performed at supplementary feeding stations with data derived from population matrix-modelling approximations. Our results suggest that visual surveys overestimate the number of immature (<2 years old) birds, whereas subadults (3–5 y.o.) and adults (>6 y.o.) were underestimated in comparison with the predictions of a population model using a stable-age distribution. In addition, we found that visual surveys did not provide conclusive information on true variations in the size of the focal population. Our results suggest that although long-term studies (i.e. population matrix modelling based on capture-recapture procedures) are a more time-consuming method, they provide more reliable and robust estimates of population parameters needed in designing and applying conservation strategies. The findings shown here are likely transferable to the management and conservation of other long-lived vertebrate populations that share similar life-history traits and ecological requirements.

Cascading climate effects and related ecological consequences during past centuries

The interface between climate and ecosystem structure and function is incompletely understood, partly because few ecological records start before the recent warming phase. Here, we analyse an exceptional 100-yr long record of the great tit (Parus major) population in Switzerland in relation to climate and habitat phenology. Using structural equation analysis, we demonstrate an uninterrupted cascade of significant influences of the large-scale atmospheric circulation (North-Atlantic Oscillation, NAO, and North-sea – Caspian Pattern, NCP) on habitat and breeding phenology, and further on fitness-relevant life history traits within great tit populations. We then apply the relationships of this analysis to reconstruct the circulation-driven component of fluctuations in great tit breeding phenology and productivity on the basis of new seasonal NAO and NCP indices back to 1500 AD. According to the structural equation model, the multi-decadal oscillation of the atmospheric circulation likely led to substantial variation in habitat phenology, productivity and consequently, tit population fluctuations with minima during the "Maunder Minimum" (∼ 1650–1720) and the Little Ice Age Type Event I (1810–1850). The warming since 1975 was not only related with a quick shift towards earlier breeding, but also with the highest productivity since 1500, and thus, the impact of the NAO and NCP has contributed to an unprecedented increase of the population. A verification of the structural equation model against two independent data series (1970–2000 and 1750–1900) corroborates that the retrospective model reliably depicts the major long-term NAO/NCP impact on ecosystem parameters. The results suggest a complex cascade of climate effects beginning at a global scale and ending at the level of individual life histories. This sheds light on how large-scale climate conditions substantially affect major life history parameters within a population, and thus influence key ecosystem parameters at the scale of centuries.

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

The patterns of genomic divergence during ecological speciation are shaped by a combination of evolutionary forces. Processes such as genetic drift, local reduction of gene flow around genes causing reproductive isolation, hitchhiking around selected variants, variation in recombination and mutation rates are all factors that can contribute to the heterogeneity of genomic divergence. On the basis of 60 fully sequenced three-spined stickleback genomes, we explore these different mechanisms explaining the heterogeneity of genomic divergence across five parapatric lake and river population pairs varying in their degree of genetic differentiation. We find that divergent regions of the genome are mostly specific for each population pair, while their size and abundance are not correlated with the extent of genome-wide population differentiation. In each pair-wise comparison, an analysis of allele frequency spectra reveals that 25–55% of the divergent regions are consistent with a local restriction of gene flow. Another large proportion of divergent regions (38–75%) appears to be mainly shaped by hitchhiking effects around positively selected variants. We provide empirical evidence that alternative mechanisms determining the evolution of genomic patterns of divergence are not mutually exclusive, but rather act in concert to shape the genome during population differentiation, a first necessary step towards ecological speciation.

Development and characterization of novel microsatellite markers for Arion slug species

Seventeen polymorphic microsatellite markers were isolated and characterized in Arion vulgaris/lusitanicus, which belongs to the worst European slug pests with serious economic and ecological impact. These markers were tested on 23 individuals collected in a population in Switzerland. Numbers of alleles ranged from 2 to 14 per locus, observed and expected heterozygosities ranged from 0.174 to 0.87, and from 0.162 to 0.903, respectively. These loci were also successfully amplified and were polymorphic in the closely related species A. rufus and A. ater. These loci represent the first highly polymorphic nuclear markers described for A. vulgaris and pave the way for population genetics and molecular ecology research of the important Arion pest slugs.