P-233-Biodiversity of mucosa associated microbiome of Crohn's disease patients living in middle western São Paulo State, Brazil

Background: The intestinal microbiome (IM) has extensively been studied in the search for a link of bacteria with the cause of Crohn`s disease (CD). The association might result from the action of a specific pathogen and/or an eventual imbalance in bacterial species composition of the gut. The innumerous virulence associated markers and strategies described for adherent and invasive Escherichia coli (AIEC) have made them putative candidate pathogens for CD. IM of CD patients shows dysbiosis, manifested by the proliferation of bacterial groups such as Enterobacteriaceae and reduction of others such as Lactobacillus and Bifidobacterium. The augmented bacterial population comprising of commensal and/or pathogenic organisms super stimulates the immune system, triggering the inflammatory reactions responsible for the clinical manifestations of the disease. Considering the role played by IM in CD and the multiple variables influencing its species composition, resulting in differences among populations, the objective of this study was to determine the bacterial biodiversity in the mucosa associated microbiome of CD patients from a population not previously subject to this analysis, living in the middle west region of Sao Paulo state. Methods: A total of 4 CD patients and 5 controls subjects attending the Botucatu Medical School of the Sao Paulo State University (UNESP) for routine colonoscopy and who signed an informed consent were included in the study. A number of 2 biopsies, one from the ileum and other from any part of the terminal colon, were taken from each subject and immediately frozen at -70[degrees]C until DNA purification. The bacterial biodiversity was assessed by next generation (ion torrent) sequencing of PCR amplicons of the ribosomal DNA 16S V6 region (16S V6 rDNA). The bacterial identification was performed at the genus level, by alignment of the generated DNA sequences with those available at the ribosomal database project (RDP) website. Results: The overall DNA sequence output was based on an average number of 526,427 reads per run, matching 50 bacterial genus 16SrDNA sequences available at the RDB website, and 22 non matching sequences. Over 95% of the sequences corresponded to taxa belonging to the major phyla: Firmicutes, Bacterioidetes, Proteobacteria and Actinobacteria. Irrespective of the intestinal site analyzed, no case-control differences could be observed in the prevalence of Actinobacteria and Firmicutes. The prevalence of Proteobacteria was higher (40%) in the biopsies of control subjects as compared to that of DC patients (16%). For Bacterioidetes, the higher prevalence was observed among DC patients (33% as opposed to 14,5% in controls). The significance for all comparisons considered a p value < 0,05 in a Chi2 test. No mucosal site specific differences could be observed in IM comparisons of CD and control subjects. Conclusions: The rise in the number of Bacterioidetes observed here among CD patients seems to be in agreement with most of studies published thus far. Yet, the reduction in the number of Proteobacteria along with an apparently unaltered population of Actinobacteria and Firmicutes, which include the so called "beneficial" organisms Bifidobacterium and Lactobacillus were rather surprising. These data suggest that the analyses on the role of IM in CD should consider the multiple variables that may influence its species composition.

Genética populacional de Myrmecophaga tridactyla (Pilosa, Myrmecophagidae) no estado de São Paulo utilizando o gene mitocondrial CytB

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Mating system parameters at hierarchical levels of fruits, individuals and populations in the Brazilian insect-pollinated tropical tree, Tabebuia roseo-alba (Bignoniaceae)

For many tree species, mating system analyses have indicated potential variations in the selfing rate and paternity correlation among fruits within individuals, among individuals within populations, among populations, and from one flowering event to another. In this study, we used eight microsatellite markers to investigate mating systems at two hierarchical levels (fruits within individuals and individuals within populations) for the insect pollinated Neotropical tree Tabebuia roseo-alba. We found that T. roseo-alba has a mixed mating system with predominantly outcrossed mating. The outcrossing rates at the population level were similar across two T. roseo-alba populations; however, the rates varied considerably among individuals within populations. The correlated paternity results at different hierarchical levels showed that there is a high probability of shared paternal parentage when comparing seeds within fruits and among fruits within plants and full-sibs occur in much higher proportion within fruits than among fruits. Significant levels of fixation index were found in both populations and biparental inbreeding is believed to be the main cause of the observed inbreeding. The number of pollen donors contributing to mating was low. Furthermore, open-pollinated seeds varied according to relatedness, including half-sibs, full-sibs, self-sibs and self- half-sibs. In both populations, the effective population size within a family (seed-tree and its offspring) was lower than expected for panmictic populations. Thus, seeds for ex situ conservation genetics, progeny tests and reforestation must be collected from a large number of seed-trees to guarantee an adequate effective population in the sample.

Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity

The time is ripe for a comprehensive mission to explore and document Earth's species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is attainable based on the strength of 250 years of progress, worldwide collections, existing experts, technological innovation and collaborative teamwork. Existing digitization projects are overcoming obstacles of the past, facilitating collaboration and mobilizing literature, data, images and specimens through cyber technologies. Charting the biosphere is enormously complex, yet necessary expertise can be found through partnerships with engineers, information scientists, sociologists, ecologists, climate scientists, conservation biologists, industrial project managers and taxon specialists, from agrostologists to zoophytologists. Benefits to society of the proposed mission would be profound, immediate and enduring, from detection of early responses of flora and fauna to climate change to opening access to evolutionary designs for solutions to countless practical problems. The impacts on the biodiversity, environmental and evolutionary sciences would be transformative, from ecosystem models calibrated in detail to comprehensive understanding of the origin and evolution of life over its 3.8 billion year history. The resultant cyber-enabled taxonomy, or cybertaxonomy, would open access to biodiversity data to developing nations, assure access to reliable data about species, and change how scientists and citizens alike access, use and think about biological diversity information.

Wireless systems for the fourth generation

Today, third generation networks are consolidated realities, and user expectations on new applications and services are becoming higher and higher. Therefore, new systems and technologies are necessary to move towards the market needs and the user requirements. This has driven the development of fourth generation networks. ”Wireless network for the fourth generation” is the expression used to describe the next step in wireless communications. There is no formal definition for what these fourth generation networks are; however, we can say that the next generation networks will be based on the coexistence of heterogeneous networks, on the integration with the existing radio access network (e.g. GPRS, UMTS, WIFI, ...) and, in particular, on new emerging architectures that are obtaining more and more relevance, as Wireless Ad Hoc and Sensor Networks (WASN). Thanks to their characteristics, fourth generation wireless systems will be able to offer custom-made solutions and applications personalized according to the user requirements; they will offer all types of services at an affordable cost, and solutions characterized by flexibility, scalability and reconfigurability. This PhD’s work has been focused on WASNs, autoconfiguring networks which are not based on a fixed infrastructure, but are characterized by being infrastructure less, where devices have to automatically generate the network in the initial phase, and maintain it through reconfiguration procedures (if nodes’ mobility, or energy drain, etc..., cause disconnections). The main part of the PhD activity has been focused on an analytical study on connectivity models for wireless ad hoc and sensor networks, nevertheless a small part of my work was experimental. Anyway, both the theoretical and experimental activities have had a common aim, related to the performance evaluation of WASNs. Concerning the theoretical analysis, the objective of the connectivity studies has been the evaluation of models for the interference estimation. This is due to the fact that interference is the most important performance degradation cause in WASNs. As a consequence, is very important to find an accurate model that allows its investigation, and I’ve tried to obtain a model the most realistic and general as possible, in particular for the evaluation of the interference coming from bounded interfering areas (i.e. a WiFi hot spot, a wireless covered research laboratory, ...). On the other hand, the experimental activity has led to Throughput and Packet Error Rare measurements on a real IEEE802.15.4 Wireless Sensor Network.

Genetic dynamics across early life stages in the tropical tree Prunus africana (Rosaceae)

In many plant species, the genetic template of early life-stages is formed by animal-mediated pollination and seed dispersal and has profound impact on further recruitment and population dynamics. Understanding the impact of pollination and seed dispersal on genetic patterns is a central issue in plant population biology. In my thesis, I investigated (i) contemporary dispersal and gene flow distances as well as (ii) genetic diversity and spatial genetic structure (SGS) across subsequent recruitment stages in a population of the animal-pollinated and dispersed tree Prunus africana in Kakamega Forest, West Kenya. Using microsatellite markers and parentage analyses, I inferred distances of pollen dispersal (father-to-mother), seed dispersal/maternal gene flow (mother-to-offspring) as well as paternal gene flow (father-to-offspring) for four early life stages of the species (seeds and fruits, current year seedlings, seedlings ≤ 3yr, seedlings > 3yr). Distances of pollen and seed dispersal as well as paternal gene flow were significantly shorter than expected from the spatial arrangement of trees and sampling plots. They were not affected by the density of conspecific trees in the surrounding. At the propagule stage, mean pollen dispersal distances were considerably (23-fold) longer than seed dispersal distances, and paternal gene flow distances exceeded maternal gene flow by a factor of 25. Seed dispersal distances were remarkably restricted, potentially leading to a strong initial SGS. The initial genetic template created by pollination and seed dispersal was extensively altered during later recruitment stages. Potential Janzen-Connell effects led to markedly increasing distances between offspring and both parental trees in older life stages. This showed that distance and density-dependent mortality factors are not exclusively related to the mother tree, but also to the father. Across subsequent recruitment stages, the pollen to seed dispersal ratio and the paternal to maternal gene flow ratio dropped to 2.1 and 3.4, respectively, in seedlings > 3yr. The relative changes in effective pollen dispersal, seed dispersal, and paternal gene flow distances across recruitment stages elucidate the mechanisms affecting the contribution of the two processes pollen and seed dispersal to overall gene flow. Using the same six microsatellite loci, I analyzed genetic diversity and SGS across five life stages, from seed rain to adults. Levels of genetic diversity within the studied P. africana population were comparable to other Prunus species and did not vary across life stages. In congruence with the short seed dispersal distances, I found significant SGS in all life stages. SGS decreased from seed and early seedling stages to older juvenile stages, and it was higher in adults than in late juveniles of the next generation. A comparison of the data with direct assessments of contemporary gene flow patterns indicate that distance- or density-dependent mortality, potentially due to Janzen-Connell effects, led to the initial decrease in SGS. Intergeneration variation in SGS could have been driven by variation in demographic processes, the effect of overlapping generations, and local selection processes. Overall, my study showed that complex sequential processes during recruitment contribute to the spatial genetic structure of tree populations. It highlights the importance of a multistage perspective for a comprehensive understanding of the impact of animal-mediated pollen and seed dispersal on spatial population dynamics and genetic patterns of trees.

Unmittelbare, dauerhafte sowie evolutionäre Anpassung an Fremdstoffexpositionen

Eine der Hauptursachen für unerwünschte oder reduzierte Wirkungen von Medikamenten ist die Induktion von Enzymen und Transportern des Medikamentenstoffwechsels. Diese Induktion stellt ursprünglich eine physiologische Reaktion auf die Aufnahme von potentiell schädlichen Fremdstoffen aus der Umwelt dar und sichert so die Gesundheit und Fortpflanzungsfähigkeit von Lebewesen. Beim Menschen sowie anderen Säugetieren werden Fremdstoffe hauptsächlich von den nukleären Rezeptoren PXR und CAR in der Leber und im Dünndarm detektiert. Zu den Medikamenten, welche über PXR und CAR wirken, gehören unter anderem Antikonvulsiva, Statine, antiretrovirale Medikamente, Glucocorticoide sowie Antimykotika. Die durch Fremdstoffe aktivierten Transkriptionsfaktoren PXR und CAR steigern die Menge der Enzyme und Transporter des Fremdstoffmetabolismus. Hierzu zählen vor allem die Cytochrom P450-Enzyme (Cyp-Enzyme) mit breitem Substratspektrum oder der Transporter MDR1, welcher eine Vielzahl von Substraten über Membranen transportiert. Durch die Biotransformation werden die induzierenden, lipophilen Substanzen so modifiziert, dass sie leichter über den Urin oder die Galle ausgeschieden werden können. \r\nDie Dauer der Induktion sollte auf die Zeit der Fremdstoffexposition beschränkt sein, um Störungen des endogenen Stoffwechsels zu vermindern. In dieser Arbeit werden jedoch Hinweise auf dauerhafte und sogar generationsübergreifende Effekte von Medikamenten in Mäusen geliefert. Nachkommen von Müttern, welche bereits vor ihrer Verpaarung einmalig mit TCPOBOP, einem Liganden des murinen CAR, injiziert wurden, hatten eine ungefähr 100-fach gesteigerte Genexpression von Cyp2b10. Auch gab es Expressionsänderungen von Genen, deren Produkte eine Rolle im Lipidstoffwechsel sowie bei Immunkrankheiten spielen. Eine Hochdurchsatz-RNA-Sequenzierung der injizierten Elterngeneration ergab außerdem dauerhafte Expressionsveränderungen anderer Gene des Medikamentenstoffwechsels sowie von Genen mit Verbindung zum Energiemetabolismus. \r\nBerücksichtigt man die enge evolutionäre Verwandtschaft der nukleären Rezeptoren CAR und PXR, sind Langzeitveränderungen auch für PXR möglich und wurden im Verlauf dieser Arbeit ebenfalls untersucht. Eine Hochdurchsatz-Sequenzierung ergab für Mäuse, welche mit dem PXR-Aktivator PCN induziert wurden, dass selbst noch drei Monate nach der Exposition Gene verändert exprimiert waren, welche im Zusammenhang mit Lebernekrosen stehen. Bei Nachkommen von PCN-injizierten Müttern wurden Gene unterschiedlich exprimiert, welche eine Rolle bei der Energiehomöostase sowie im Glukosestoffwechsel spielen. Im Erwachsenenalter sind bei diesen Nachkommen darüber hinaus noch Gene unterschiedlich exprimiert, deren Produkte eine Funktion in der Immunantwort haben. \r\nDa Erwachsene aufgrund ihrer Lebensdauer sowie der absoluten Krankheitshäufigkeit wesentlich öfter Kontakt mit Fremdstoffen haben, war medizinisch von besonderem Interesse, ob anhaltende Genexpressionsänderungen auch bei Erwachsenen zu beobachten sind. So konnte im Rahmen dieser Arbeit gezeigt werden, dass auch einmalig exponierte Adulttiere Gene dauerhaft verändert exprimieren und die Veränderungen im Medikamentenstoffwechsel an die nächste Generation übertrugen. \r\n\r\nBisher sind klinische Studien zur Risikobewertung von Medikamenten (Pharmakovigilanz) nicht generationsübergreifend angelegt. Diese Arbeit gibt Anstöße dafür, dass dies in Zukunft für viel mehr Medikamente notwendig werden könnte. Neben Veränderungen im Medikamentenstoffwechsel ergeben sich Nebenwirkungen von PXR- und CAR-Liganden vor allem aus ihrer Beteiligung an endogenen Stoffwechselwegen. Nach Aktivierung von CAR, welcher viele metabolische Stoffwechselwege steuert, treten beispielsweise Störungen des Energiestoffwechsels auf. Ein tieferes Verständnis der Rezeptoraktivität von CAR samt einer gezielten Modulierung seiner Aktivität würde wichtige Beiträge zum Verständnis der Regulation des Fremdstoffmetabolismus sowie der Entstehung von Nebenwirkungen durch eine Behandlung mit CAR-Liganden leisten. Dauerhafte Veränderungen endogener Stoffwechselwege könnten dann möglicherweise über eine pharmakologische Modulierung der CAR-Aktivität reduziert werden. \r\nZu diesem Zweck wurden im Verlauf dieser Arbeit die CAR-Rezeptoren der Amphibien (Xenopus tropicalis, Xenopus laevis) und Reptilien (Anolis carolinensis) erstmals kloniert, als Proteine exprimiert und charakterisiert. Vergleiche zwischen Tierarten ermöglichen ein besseres Verständnis von humanen Proteinen. Funktionelle Analysen ergaben Ähnlichkeiten des Xenopus laevis-CAR mit dem PXR der Säugetiere: eine niedrige basale Aktivität sowie eine starke Induzierbarkeit durch Liganden. In weiteren funktionellen Analysen wurden die Determinanten der basalen Aktivität des Xenopus laevis-CAR untersucht. Die basale Aktivität war nicht abhängig von der subzellulären Lokalisation, sondern ergab sich aus der Proteinstruktur, welche nur beim CAR der Landvertebraten in einer aktiven Konformation fixiert ist. Ähnlich dem PXR der Säugetiere besitzt CAR der Amphibien eine Aktivierungsdomäne, welche erst durch Ligandenbindung in eine aktive Konformation gebracht wird. Mutationen einzelner Aminosäuren zum jeweils humanen Homolog erhöhten die basale Aktivität des Xenopus laevis-CAR auf die des humanen Rezeptors. Diese Mutanten mit erhöhter basalen Aktivität zeigten eine verstärkte Interaktion mit dem Kofaktor PGC-1a, einem Regulator des Energiestoffwechsels bei Säugetieren. Die hepatischen Zielgene des CAR der Amphibien überlappen zum Teil mit den humanen Zielgenen und spielen ebenfalls eine Rolle im Energiestoffwechsel.

STATISTICAL METHODS FOR RARE AND COMMON VARIANT ASSOCIATION STUDIES

Complex human diseases are a major challenge for biological research. The goal of my research is to develop effective methods for biostatistics in order to create more opportunities for the prevention and cure of human diseases. This dissertation proposes statistical technologies that have the ability of being adapted to sequencing data in family-based designs, and that account for joint effects as well as gene-gene and gene-environment interactions in the GWA studies. The framework includes statistical methods for rare and common variant association studies. Although next-generation DNA sequencing technologies have made rare variant association studies feasible, the development of powerful statistical methods for rare variant association studies is still underway. Chapter 2 demonstrates two adaptive weighting methods for rare variant association studies based on family data for quantitative traits. The results show that both proposed methods are robust to population stratification, robust to the direction and magnitude of the effects of causal variants, and more powerful than the methods using weights suggested by Madsen and Browning [2009]. In Chapter 3, I extended the previously proposed test for Testing the effect of an Optimally Weighted combination of variants (TOW) [Sha et al., 2012] for unrelated individuals to TOW &ndash F, TOW for Family &ndash based design. Simulation results show that TOW &ndash F can control for population stratification in wide range of population structures including spatially structured populations, is robust to the directions of effect of causal variants, and is relatively robust to percentage of neutral variants. In GWA studies, this dissertation consists of a two &ndash locus joint effect analysis and a two-stage approach accounting for gene &ndash gene and gene &ndash environment interaction. Chapter 4 proposes a novel two &ndash stage approach, which is promising to identify joint effects, especially for monotonic models. The proposed approach outperforms a single &ndash marker method and a regular two &ndash stage analysis based on the two &ndash locus genotypic test. In Chapter 5, I proposed a gene &ndash based two &ndash stage approach to identify gene &ndash gene and gene &ndash environment interactions in GWA studies which can include rare variants. The two &ndash stage approach is applied to the GAW 17 dataset to identify the interaction between KDR gene and smoking status.

A novel FIP1L1-PDGFRA mutant destabilizing the inactive conformation of the kinase domain in chronic eosinophilic leukemia/hypereosinophilic syndrome

BACKGROUND: The Fip1-like-1-platelet-derived growth factor receptor alpha (FIP1L1-PDGFRA) gene fusion is a common cause of chronic eosinophilic leukemia (CEL)/hypereosinophilic syndrome (HES), and patients suffering from this particular subgroup of CEL/HES respond to low-dose imatinib therapy. However, some patients may develop imatinib resistance because of an acquired T674I mutation, which is believed to prevent drug binding through steric hindrance. METHODS: In an imatinib resistant FIP1L1-PDGFRA positive patient, we analyzed the molecular structure of the fusion gene and analyzed the effect of several kinase inhibitors on FIP1L1-PDGFRA-mediated proliferative responses in vitro. RESULTS: Sequencing of the FIP1L1-PDGFRA fusion gene revealed the occurrence of a S601P mutation, which is located within the nucleotide binding loop. In agreement with the clinical observations, imatinib did not inhibit the proliferation of S601P mutant FIP1L1-PDGFRA-transduced Ba/F3 cells. Moreover, sorafenib, which has been described to inhibit T674I mutant FIP1L1-PDGFRA, failed to block S601P mutant FIP1L1-PDGFRA. Structural modeling revealed that the newly identified S601P mutated form of PDGFRA destabilizes the inactive conformation of the kinase domain that is necessary to bind imatinib as well as sorafenib. CONCLUSIONS: We identified a novel mutation in FIP1L1-PDGFRA resulting in both imatinib and sorafenib resistance. The identification of novel drug-resistant FIP1L1-PDGFRA variants may help to develop the next generation of target-directed compounds for CEL/HES and other leukemias.

Non-phenotypic tests to detect and characterize antibiotic resistance mechanisms in Enterobacteriaceae

In the past 2 decades, we have observed a rapid increase of infections due to multidrug-resistant Enterobacteriaceae. Regrettably, these isolates possess genes encoding for extended-spectrum β-lactamases (e.g., blaCTX-M, blaTEM, blaSHV) or plasmid-mediated AmpCs (e.g., blaCMY) that confer resistance to last-generation cephalosporins. Furthermore, other resistance traits against quinolones (e.g., mutations in gyrA and parC, qnr elements) and aminoglycosides (e.g., aminoglycosides modifying enzymes and 16S rRNA methylases) are also frequently co-associated. Even more concerning is the rapid increase of Enterobacteriaceae carrying genes conferring resistance to carbapenems (e.g., blaKPC, blaNDM). Therefore, the spread of these pathogens puts in peril our antibiotic options. Unfortunately, standard microbiological procedures require several days to isolate the responsible pathogen and to provide correct antimicrobial susceptibility test results. This delay impacts the rapid implementation of adequate antimicrobial treatment and infection control countermeasures. Thus, there is emerging interest in the early and more sensitive detection of resistance mechanisms. Modern non-phenotypic tests are promising in this respect, and hence, can influence both clinical outcome and healthcare costs. In this review, we present a summary of the most advanced methods (e.g., next-generation DNA sequencing, multiplex PCRs, real-time PCRs, microarrays, MALDI-TOF MS, and PCR/ESI MS) presently available for the rapid detection of antibiotic resistance genes in Enterobacteriaceae. Taking into account speed, manageability, accuracy, versatility, and costs, the possible settings of application (research, clinic, and epidemiology) of these methods and their superiority against standard phenotypic methods are discussed.

Properties of seawater and particulate matter from a WETLabs ALFA hyperspectral laser spectrofluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with an Aquatic Laser Fluorescence Analyzer (ALFA) (Chekalyuk et al., 2014), connected in-line to the TARA flow through system during 2013. The ALFA instrument provides dual-wavelength excitation (405 and 514 nm) of laser-stimulated emission (LSE) for spectral and temporal analysis. It offers in vivo fluorescence assessments of phytoplankton pigments, biomass, photosynthetic yield (Fv/Fm), phycobiliprotein (PBP)-containing phytoplankton groups, and chromophoric dissolved organic matter (CDOM) (Chekalyuk and Hafez, 2008; 2013A). Spectral deconvolution (SDC) is used to assess the overlapped spectral bands of aquatic fluorescence constituents and water Raman scattering (R). The Fv/Fm measurements are spectrally corrected for non-chlorophyll fluorescence background produced by CDOM and other constituents (Chekalyuk and Hafez, 2008). The sensor was cleaned weakly following the manufacturer recommended protocol.

Removing exogenous information using pedigree data

Management of certain populations requires the preservation of its pure genetic background. When, for different reasons, undesired alleles are introduced, the original genetic conformation must be recovered. The present study tested, through computer simulations, the power of recovery (the ability for removing the foreign information) from genealogical data. Simulated scenarios comprised different numbers of exogenous individuals taking partofthe founder population anddifferent numbers of unmanaged generations before the removal program started. Strategies were based on variables arising from classical pedigree analyses such as founders? contribution and partial coancestry. The ef?ciency of the different strategies was measured as the proportion of native genetic information remaining in the population. Consequences on the inbreeding and coancestry levels of the population were also evaluated. Minimisation of the exogenous founders? contributions was the most powerful method, removing the largest amount of genetic information in just one generation.However, as a side effect, it led to the highest values of inbreeding. Scenarios with a large amount of initial exogenous alleles (i.e. high percentage of non native founders), or many generations of mixing became very dif?cult to recover, pointing out the importance of being careful about introgression events in population

Targeting genetic resource conservation in widespread species: a case study of Cedrela odorata L.

Conservation of genetic resources is a recognised necessity for the long term maintenance of evolutionary potential. Effective assessment and implementation Strategies are required to permit rapid evaluation and protection of resources. Here we use information from the chloroplast, total genome and quantitative characters assayed across wide-ranging populations to assess genetic resources in a Neotropical tree, Cedrela odorata. A major differentiation identified for organelle, total genomic and quantitative variation was found to coincide with an environmental gradient across Costa Rica. However, a major evolutionary divergence between the Yucatan region and Honduras/Nicaragua identified within the chloroplast genome was not differentiated using quantitative characters. Based on these and other results, a three-tiered conservation genetic prioritisation process is recommended. In order of importance, and where information is available, conservation units should be defined using quantitative (expressed genes), nuclear (genetic connectivity) and organellar (evolutionary) measures. Where possible, information from range wide and local scale studies should be combined and emphasis should be placed on coincidental disjunctions for two or more measures. However, if only rapid assessments of diversity are possible, then assessment of organelle variation provides the most cautious assessment of genetic resources, at least for C. odorata, and can be used to propose initial conservation units. When considering effective implementation of genetic resource management strategies a final tier should be considered, that of landuse/geopolitical divisions. (C) 2004 Elsevier B.V. All rights reserved.

Reduced genetic diversity and significant genetic differentiation after translocation: Comparison of the remnant and translocated populations of bridled nailtail wallabies (Onychogalea fraenata)

Loss of genetic diversity and increased population differentiation from source populations are common problems associated with translocation programmes established from captive-bred stock or a small number of founders. The bridled nailtail wallaby is one of the most endangered macropods in Australia, having been reduced to a single remnant population in the last 100 years. A translocated population of bridled nailtail wallabies was established using animals sourced directly from the remnant population (wild-released) as well as the progeny of animals collected for a captive breeding programme (captive-bred). The aims of this study were to compare genetic diversity among released animals and their wild-born progeny to genetic diversity observed in the remnant population, and to monitor changes in genetic diversity over time as more animals were released into the population. Heterozygosity did not differ between the translocated and remnant population; however, allelic diversity was significantly reduced across all released animals and their wild-born progeny. Animals bred in captivity and their wild-born progeny were also significantly differentiated from the source population after just four generations. Wild-released animals, however, were representative of the source population and several alleles were unique to this group. Both heterozygosity and allelic diversity among translocated animals decreased over time with the additional release of captive-bred animals, as no new genetic stock was added to the population. Captive breeding programmes can provide large numbers of animals for release, but this study highlights the importance of sourcing animals directly from remnant populations in order to maintain genetic diversity and minimise genetic drift.

Significant patterns of population genetic structure and limited gene flow in a threatened macropodid marsupial despite continuous habitat in southeast Queensland, Australia

Many endangered species worldwide are found in remnant populations, often within fragmented landscapes. However, when possible, an understanding of the natural extent of population structure and dispersal behaviour of threatened species would assist in their conservation and management. The brush-tailed rock-wallaby (Petrogale penicillata), a once abundant and widespread rock-wallaby species across southeastern Australia, has become nearly extinct across much of the southern part of its range. However, the northern part of the species' range still sustains many small colonies closely distributed across suitable habitat, providing a rare opportunity to investigate the natural population dynamics of a listed threatened species. We used 12 microsatellite markers to investigate genetic diversity, population structure and gene flow among brush-tailed rock-wallaby colonies within and among two valley regions with continuous habitat in southeast Queensland. We documented high and signifcant levels of population genetic structure between rock-wallaby colonies embedded in continuous escarpment habitat and forest. We found a strong and significant pattern of isolation-by-distance among colonies indicating restricted gene flow over a small geographic scale (< 10 km) and conclude that gene flow is more likely limited by intrinsic factors rather than environmental factors. In addition, we provide evidence that genetic diversity was significantly lower in colonies located in a more isolated valley region compared to colonies located in a valley region surrounded by continuous habitat. These findings shed light on the processes that have resulted in the endangered status of rock-wallaby species in Australia and they have strong implications for the conservation and management of both the remaining 'connected' brush-tailed rock-wallaby colonies in the northern parts of the species' range and the remnant endangered populations in the south.