Population genetic structure and mating system of Swietenia macrophylla King (Meliaceae) in the Brazilian Amazon : implications for conservation

Mahogany, Swietenia macrophylla (Meliaceae) is the most valuable hardwood species in Neotropics and is seriously threatened owing to over-exploitation and habitat destruction. The population genetic structure and mating system of S. macrophylla were studied in the Brazilian Amazon for conservation purposes. Ten highly polymorphic micro satellite markers were developed from an enriched genomic library of S. macrophylla and combined in three multiplexed fluorescence based genotyping systems. The number of alleles per locus ranged from 11 to 25 (mean = 15.8). The probability of genetic identity (7x10- 15) and the probability of paternity exclusion (0.999998) found over all loci indicate the high discriminating power of these markers. The genetic structure was investigated in seven populations 8- 2,103 km apart. High genetic diversity was detected within populations (mean He = 0.761, range 0.719-0.800) and a significant level of inbreeding was found (f = 0.046, P<0.0001, range 0.014-0.097) indicating nonrandom mating of individuals within populations. Genetic differentiation among populations was significant (A = 0.12 and p = 0.14, P<0.0001), but no clear pattern of isolation by distance was found. Conservation strategies for mahogany should take into account the existence of important genetic structuring of populations. S. macrophylla seems to have adaptations that preferentially produce outcrossed progeny but also allows for selfing. The high multilocus outcrossing rate (tm = 0.958) estimated for one population indicated that, although there was a prevalence of outcrossing, selfing was not negligible. Around 4-6% of seedlings in the population were likely to have resulted from self-fertilization and substantial biparental inbreeding was denoted by the significant difference between the multilocus and singlelocus estimates (tm - ts = 0.14). Owing to the species pre-adaptation to colonize newly open, disturbed habitats, many of the remaining trees in logged areas may persist as viable individuals which could be very important for population recovery and genetic conservation programmes

Extreme long-distance dispersal of the lowland tropical rainforest tree Ceiba pentandra L. (Malvaceae) in Africa and the Neotropics

Many tropical tree species occupy continental expanses of rainforest and flank dispersal barriers such as oceans and mountains. The role of long-distance dispersal in establishing the range of such species is poorly understood. In this study, we test vicariance hypotheses for range disjunctions in the rainforest tree Ceiba pentandra , which is naturally widespread across equatorial Africa and the Neotropics. Approximate molecular clocks were applied to nuclear ribosomal [ITS (internal transcribed spacer)] and chloroplast ( psb B- psb F) spacer DNA sampled from 12 Neotropical and five West African populations. The ITS ( N  = 5) and psb B- psb F ( N  = 2) haplotypes exhibited few nucleotide differences, and ITS and psb B- psb F haplotypes were shared by populations on both continents. The low levels of nucleotide divergence falsify vicariance explanations for transatlantic and cross-Andean range disjunctions. The study shows how extreme long-distance dispersal, via wind or marine currents, creates taxonomic similarities in the plant communities of Africa and the Neotropics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71417/1/j.1365-294X.2007.03341.x.pd

Prey preference of the common vampire bat (Desmodus rotundus, Chiroptera) using molecular analysis

Morphological identification of prey fragments in vampire bat feces is impossible because of an exclusively blood-based diet. Therefore, studies of their foraging ecology require innovative approaches. We investigated the diet of Desmodus rotundus using a PCR-restriction fragment length polymorphism (RFLP) molecular method by amplifying the cytochrome b mitochondrial gene (380 bp) from DNA fecal samples collected from captive bats fed with blood from chickens, cattle, pigs, dogs, and humans - the 5 most frequently attacked prey species in rural areas of the Brazilian Amazonia. The prey preference of the vampire bat was investigated in 18 riverine villages, where the availability of domestic animals to bats was quantified. Prey DNA amplified from fecal samples exhibited no visible signals of vampire bat DNA. A PCR - RFLP flowchart and a combination of 2 DNA restriction enzymes allowed the direct identification of prey to species level. The enzymes' restriction profile did not overlap with those of vampire bats or wild mammal and avian species. Chickens were the most attacked prey species (61.4% of the identifications, n = 27), but pigs were highly preferred in relation to prey availability. This suggests a preference for mammalian blood in D. rotundus diet, with chickens exploited as a secondary food source. No wild vertebrate species was identified in the fecal samples, indicating that vampire bats are selectively feeding on the blood of domesticated animals, probably because they are more predictable and easily accessed resources. © 2015 American Society of Mammalogists

Conservation implications of the mating system of the Pampa Hermosa landrace of peach palm analyzed with microsatellite markers

Peach palm (Bactris gasipaes) is cultivated by many indigenous and traditional communities from Amazonia to Central America for its edible fruits, and is currently important for its heart-of-palm. The objective of this study was to investigate the mating system of peach palm, as this is important for conservation and breeding. Eight microsatellite loci were used to genotype 24 open-pollinated progenies from three populations of the Pampa Hermosa landrace maintained in a progeny trial for genetic improvement. Both the multi-locus outcrossing rates (0.95 to 0.99) and the progeny level multi-locus outcrossing rates (0.9 to 1.0) were high, indicating that peach palm is predominantly allogamous. The outcrossing rates among relatives were significantly different from zero (0.101 to 0.202), providing evidence for considerable biparental inbreeding within populations, probably due to farmers planting seeds of a small number of open-pollinated progenies in the same plot. The correlations of paternity estimates were low (0.051 to 0.112), suggesting a large number of pollen sources (9 to 20) participating in pollination of individual fruit bunches. Effective population size estimates suggest that current germplasm collections are insufficient for long-term ex situ conservation. As with most underutilized crops, on farm conservation is the most important component of an integrated conservation strategy. © 2015, Sociedade Brasileira de Genética. Printed in Brazil

Macroevolutionary patterns in overexpression of tyrosine:An anti‐herbivore defence in a speciose tropical tree genus, Inga (Fabaceae)

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.1.Plant secondary metabolites are a key defence against herbivores, and their evolutionary origin is likely from primary metabolites. Yet for this to occur, an intermediate step of overexpression of primary metabolites would need to confer some advantage to the plant. Here, we examine the evolution of overexpression of the essential amino acid, L‐tyrosine and its role as a defence against herbivores. 2.We examined overexpression of tyrosine in 97 species of Inga (Fabaceae), a genus of tropical trees, at five sites throughout the Neotropics. We predicted that tyrosine could act as an anti‐herbivore defence because concentrations of 4% tyrosine in artificial diets halved larval growth rates. We also collected insect herbivores to determine if tyrosine and its derivatives influenced host associations. 3.Overexpression of tyrosine was only present in a single lineage comprising 21 species, with concentrations ranging from 5% to 20% of the leaf dry weight. Overexpression was pronounced in expanding but not in mature leaves. Despite laboratory studies showing toxicity of L‐tyrosine, Inga species with tyrosine suffered higher levels of herbivory. We therefore hypothesize that overexpression is only favoured in species with less effective secondary metabolites. Some tyrosine‐producing species also contained secondary metabolites that are derived from tyrosine: tyrosine‐gallates, tyramine‐gallates and DOPA‐gallates. Elevated levels of transcripts of prephenate dehydrogenase, an enzyme in the tyrosine biosynthetic pathway that is insensitive to negative feedback from tyrosine, were found only in species that overexpress tyrosine or related gallates. Different lineages of herbivores showed contrasting responses to the overexpression of tyrosine and its derived secondary metabolites in their host plants. 4.Synthesis. We propose that overexpression of some primary metabolites can serve as a chemical defence against herbivores, and are most likely to be selected for in species suffering high herbivory due to less effective secondary metabolites. Overexpression may be the first evolutionary step in the transition to the production of more derived secondary metabolites. Presumably, derived compounds would be more effective and less costly than free tyrosine as anti‐herbivore defences.National Science Foundatio

Programação da produção: Otimização de Layouts Industriais

O problema conhecido na literatura como “Facility layout problem (FLP)”, em que se pretende determinar a disposição de recursos de produção e a sua interação num determinado espaço, é um problema estratégico para a implementação do chão de fábrica de uma empresa pelo impacto que tem na performance da produção. O problema consiste em encontrar um posicionamento único entre instalações (departamentos, máquinas, células de produção, armazéns, etc.) e localizações no chão de fábrica, de forma a otimizar um ou mais objetivos de produção. O objetivo da criação de layout consiste na otimização do espaço existente, minimização do tempo de produção, redução do custo de manuseamento de matérias, aumento do grau de flexibilidade, entre outros. A solução do problema deverá especificar a localização relativa de cada departamento (layout em bloco) e numa fase posterior poderá especificar o layout detalhado dentro de cada departamento. Na presente tese serão apresentados alguns modelos matemáticos para criação de um layout, neste caso vamos usar uma formulação matemática Quadratic Assignment Problem (QAP), uma formulação matemática Mixed Integer Programming (MIP) e uma heurística de Particle Swarm Optimization (PSO) para resolver problemas de layout. Todas estas formulações e modelos serão postos em prática para a resolução de problemas fictícios. Numa primeira abordagem iremos resolver problemas fictícios onde abordaremos a formulação QAP para problemas de atribuição de espaço de duas dimensões (x,y) e MIP e em seguida iremos usar a heurística PSO para a resolução de problemas em escala maior e real.The problem known in the literature as "Facility layout problem (FLP)", which is intended to determine the physical layout of industrial facilities, is a strategic problem for the implementation of a company by the impact it has on the production performance. The problem is to find an unambiguous allocation between facilities (departments, machines, production cells, warehouses, etc.) and locations on the shop floor in order to optimize one or more production goals. The objectives often considered are the optimization of the space, minimizing production time, reduce the handling costs of materials, increased flexibility, among others. The solution of the problem should specify the relative location of each department (block layout) and at a later stage it can specify the detailed layout within each department. In this thesis will be presented some methods of resolution in this case we use a discrete Quadratic Assignment formulation (QAP), a Mixed Integer Linear Programming formulation (MIP) and a Particle Swarm Optimization heuristic (PSO) to solve layout problems. All these heuristics will be implemented for solving fictitious problems. In a first approach we will solve simpler problems where we use the QAP and MIP formulation and following we will use the PSO heuristic to solve problems on a larger scale

Conservation implications of the mating system of the Pampa Hermosa landrace of peach palm analyzed with microsatellite markers

Peach palm (Bactris gasipaes) is cultivated by many indigenous and traditional communities from Amazonia to Central America for its edible fruits, and is currently important for its heart-of-palm. The objective of this study was to investigate the mating system of peach palm, as this is important for conservation and breeding. Eight microsatellite loci were used to genotype 24 open-pollinated progenies from three populations of the Pampa Hermosa landrace maintained in a progeny trial for genetic improvement. Both the multi-locus outcrossing rates (0.95 to 0.99) and the progeny level multi-locus outcrossing rates (0.9 to 1.0) were high, indicating that peach palm is predominantly allogamous. The outcrossing rates among relatives were significantly different from zero (0.101 to 0.202), providing evidence for considerable biparental inbreeding within populations, probably due to farmers planting seeds of a small number of open-pollinated progenies in the same plot. The correlations of paternity estimates were low (0.051 to 0.112), suggesting a large number of pollen sources (9 to 20) participating in pollination of individual fruit bunches. Effective population size estimates suggest that current germplasm collections are insufficient for long-term ex situ conservation. As with most underutilized crops, on farm conservation is the most important component of an integrated conservation strategy

High genetic diversity among and within bitter manioc varieties cultivated in different soil types in Central Amazonia

Although manioc is well adapted to nutrient-poor Oxisols of Amazonia, ethnobotanical observations show that bitter manioc is also frequently cultivated in the highly fertile soils of the floodplains and Amazonian dark earths (ADE) along the middle Madeira River. Because different sets of varieties are grown in each soil type, and there are agronomic similarities between ADE and floodplain varieties, it was hypothesized that varieties grown in ADE and floodplain were more closely related to each other than either is to varieties grown in Oxisols. We tested this hypothesis evaluating the intra-varietal genetic diversity and the genetic relationships among manioc varieties commonly cultivated in Oxisols, ADE and floodplain soils. Genetic results did not agree with ethnobotanical expectation, since the relationships between varieties were variable and most individuals of varieties with the same vernacular name, but grown in ADE and floodplain, were distinct. Although the same vernacular name could not always be associated with genetic similarities, there is still a great amount of variation among the varieties. Many ecological and genetic processes may explain the high genetic diversity and differentiation found for bitter manioc varieties, but all contribute to the maintenance and amplification of genetic diversity within the manioc in Central Amazonia. © 2017, Sociedade Brasileira de Genética

Microsatellites for mahoganies: Twelve new loci for Swietenia macrophylla and its high transferability to Khaya senegalensis

Premise of the study: A new set of 12 microsatellite markers was developed and characterized for big-leaf mahogany (Swietenia macrophylla King, Meliaceae) and its transferability assayed in the African mahogany, Khaya senegalensis (Desr.) A. Juss. (Meliaceae), to study population and conservation genetics of these threatened tropical timber species. Methods and Results: Using an enriched library approach twelve novel microsatellite loci were identified for S. macrophylla. The number of alleles per locus ranged from 5 to 14 and mean observed and expected heterozygosities were 0.819 and 0.822, respectively. Twenty microsatellite loci developed for S. macrophylla (12 from this study and eight previously published) were tested for K. senegalensis and 10 polymorphic were characterized. Conclusions: The results show the highly informative content of the new SSR loci for Swietenia macrophylla and the high effectiveness of these microsatellites for population genetics, gene flow, and mating system studies in Khaya senegalensis. © 2011 Botanical Society of America