Ecosystem-Oriented Distributed Evolutionary Computing

We create a novel optimisation technique inspired by natural ecosystems, where the optimisation works at two levels: a first optimisation, migration of genes which are distributed in a peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. We consider from the domain of computer science distributed evolutionary computing, with the relevant theory from the domain of theoretical biology, including the fields of evolutionary and ecological theory, the topological structure of ecosystems, and evolutionary processes within distributed environments. We then define ecosystem- oriented distributed evolutionary computing, imbibed with the properties of self-organisation, scalability and sustainability from natural ecosystems, including a novel form of distributed evolu- tionary computing. Finally, we conclude with a discussion of the apparent compromises resulting from the hybrid model created, such as the network topology.Comment: 8 pages, 5 figures. arXiv admin note: text overlap with arXiv:1112.0204, arXiv:0712.4159, arXiv:0712.4153, arXiv:0712.4102, arXiv:0910.067

Seed systems and crop genetic diversity in agroecosystems

Poster presented at the First Diversitas Open Science Conference. Oaxaca (Mexico), 9-12 Nov 200

Tracking Plastid Gene Migration in \u3ci\u3eKarenia brevis\u3c/i\u3e

Karenia brevis is a marine dinoflagellate responsible for the harmful algal blooms (also known as red tides) in the Gulf of Mexico. K. brevis expresses antisense (AS) RNAs, each of which has a complementary region to the messenger RNA (mRNA) of a variety of genes. In dinoflagellates, many plastid (and mitochondrial) genes have migrated to the nuclear genome. It is unknown whether chloroplast genes, such as photosystem – D2, have migrated in K. brevis. It is also unknown where the gene that expresses the AS RNA for photosystem D2 resides. The protein-coding gene and the AS RNA-expressing gene could both reside in the chloroplast, both in the nucleus, or in some split combination between the two genomes. Primers designed from photosystem D2 ESTs were used in a series of RACE reactions to capture the unique regions of both photosystem – D2 AS RNA and mRNA. Gel imaging showed a distinct band for the unique 5’ end of the mRNA. Sequencing of this band will allow for the design of a probe to determine which genome houses the photosystem – D2 mRNA. This work can be furthered to compile known locations for both the mRNA and AS RNA of both chloroplast and mitochondrial genes of K. brevis

Effect of transgene introgression site on gene migration from transgenic b. napus to b. rapa [abstract]

Abstract only availableThere is a growing concern of the possible transgenic introgression from GM plants into agricultural weeds, which has stimulated research in the process of crop to weed gene flow. Crop to weed gene flow often involves the hybridization of a polyploidy crop to a diploid weed. An example is canola (Brassica napus with AACC genomes) which can hybridize with B. rapa (AA) to produce fertile triploid F1 hybrids (ACC) in the wild. It is hypothesized that there are "safe sites" on the C genome because the C genome is likely to be lost from wild populations after a few generations of repeated backcrossing with B. rapa. However, there is homoeology between the A and C genomes of Brassica, which allows potential recombination between genomes and the movement of transgenes from the C to A genomes by chromosomal rearrangements. Recent advances in molecular markers and fluorescent in situ hybridization (FISH) now allow us to observe the frequency of homoeologous exchanges following hybridization. Our research is focused on finding safe sites within the B. napus genome which are least likely to be transferred into B. napus and B. rapa hybrids and their progeny. To test this, we have crossed a transgenic B. napus with a natural B. rapa three times to make three different F1events. Then we backcrossed each of the three F1 three times with B. rapa. We are measuring the germination rate of each generation and using transgene specific PCR primers to check the presence or absence of the transgene in hybrids. We will also use molecular cytogenetics (FISH) to count chromosome numbers. This study will help determine the possibilities of a "safe" site in B. napus and offer insight in the mechanisms of crop to weed transgene introgression in B. napus x B. rapa hybrids.MU Monsanto Undergraduate Research Fellowshi

Isolated intermediates - products of long distance gene dispersal, phantom hybridity or convergent evolution? The case of the half-barked Eucalyptus amygdalina

Apparent intermediates between Eucalyptus amygdalina and E. pulchella occur well outside the recognized range of the latter species. Progenies of these isolated intermediates were grown in uniform conditions with progenies of trees of E. pulchella, E. amygdaline and apparent hybrids between these two species that are found where they occur parapatrically. The isolated intermediate population proved identical with E. amygdalina in seedling characteristics, while the parapatric intermediates were more variable than the other populations, this variability probably being partly the result of hybridization between E. amygdalina and either E. tenuiramis or E. risdonii. The allopatric intermediate population is more likely to have resulted from convergence of E. amygdalina in the direction of E. pulchella than from phantom hybridity or long distance gene migration

Seasonal variations in antibiotic resistance gene transport in the Almendares River, Havana, Cuba

Numerous studies have quantified antibiotic resistance genes (ARG) in rivers and streams around the world, and significant relationships have been shown that relate different pollutant outputs and increased local ARG levels. However, most studies have not considered ambient flow conditions, which can vary dramatically especially in tropical countries. Here, ARG were quantified in water column and sediment samples during the dry- and wet-seasons to assess how seasonal and other factors influence ARG transport down the Almendares River (Havana, Cuba). Eight locations were sampled and stream flow estimated during both seasons; qPCR was used to quantify four tetracycline, two erythromycin, and three beta-lactam resistance genes. ARG concentrations were higher in wet-season versus dry-season samples, which combined with higher flows, indicated much greater ARG transport downstream during the wet-season. However, water column ARG levels were more spatially variable in the dry-season than the wet-season, with the proximity of waste outfalls strongly influencing local ARG levels. Results confirm that dry-season sampling provides a useful picture of the impact of individual waste inputs on local stream ARG levels, whereas the majority of ARGs in this tropical river were transported downstream during the wet-season, possibly due to re-entrainment of ARG from sediments

Productivity and Breeding Strategies of Sheep in Indonesia: A Review

There are two distinct types of sheep in Indonesia: thin-tailed and fat-tailed, with some strain differentiation within each. The most important sheep breeds of Indonesia are the Javanese Thin Tail (JTT) and Javanese Fat Tail (JFT) sheep of West and East Java, respectively. Included are strains of thin tailed sheep Sumatra Thin Tailed (STT), Semarang, Garut and the Priangan sheep. The government also introduced some temperate sheep breeds (such as: Merino, Suffolk, Dorset, Suffas, Dormer, St.Croix and Barbados Blackbelly sheep). The purposes of this paper are to review the potential of productivity for local sheep and their crosses with some imported sheep breeds. The concepts of breeding strategies for sheep in Indonesia are also discussed in three parts: (1) evaluation and improvement of local breeds (2) nucleus structure, and (3) gene migration (crossbreeding)

Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars

Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs. A Bayesian approach, Minimum Spanning Tree (MST) and diversity estimator, as well as multivariate analysis based on phenotypic traits, were adopted to assess the population structure. Results: Analysis based on molecular markers showed groups linked to the phylogenetic relationship among the germplasm as well as the link with the breeding program that provided the material. Diversity estimators consistently structured the population according to a priori group estimation. The phenotypic traits only discriminated main groups with contrasting characteristics, as different subspecies, ploidy level or membership in a breeding program, but were not able to discriminate within groups. A joint molecular and phenotypic characterization analysis discriminated groups based on phenotypic classification, taxonomic category, provenance source of genotypes and genetic background. Conclusions: This paper shows the significant level of diversity existing in a parental population of potato as well as the putative phylogenetic relationships among the genotypes. The use of easily measurable phenotypic traits among highly contrasting genotypes could be a reasonable approach to estimate population structure in the initial phases of a potato breeding program.Fil: Tagliotti, Martin Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Deperi, Sofía Irene. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; ArgentinaFil: Bedogni, María Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Zhang, Ruofang. Inner Mongolia University; ChileFil: Manrique Carpintero, Norma C.. Michigan State University; Estados UnidosFil: Coombs, Joseph. Michigan State University; Estados UnidosFil: Douches, David. Michigan State University; Estados UnidosFil: Huarte, Marcelo Atilio. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; Argentin