Phantom epistasis in genomic selection: on the predictive ability of epistatic models

Genomic selection uses whole-genome marker models to predict phenotypes or genetic values for complex traits. Some of these models fit interaction terms between markers, and are therefore called epistatic. The biological interpretation of the corresponding fitted effects is not straightforward and there is the threat of overinterpreting their functional meaning. Here we show that the predictive ability of epistatic models relative to additive models can change with the density of the marker panel. In more detail, we show that for publicly available Arabidopsis and rice datasets, an initial superiority of epistatic models over additive models, which can be observed at a lower marker density, vanishes when the number of markers increases. We relate these observations to earlier results reported in the context of association studies which showed that detecting statistical epistatic effects may not only be related to interactions in the underlying genetic architecture, but also to incomplete linkage disequilibrium at low marker density (“Phantom Epistasis”). Finally, we illustrate in a simulation study that due to phantom epistasis, epistatic models may also predict the genetic value of an underlying purely additive genetic architecture better than additive models, when the marker density is low. Our observations can encourage the use of genomic epistatic models with low density panels, and discourage their biological over-interpretation.Fil: Schrauf, Matías Florián. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Cátedra de Mejoramiento Genético Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Martini, Johannes W.R.. Centro Internacional de Mejoramiento de Maíz y Trigo; MéxicoFil: Simianer, Henner. Universität Göttingen; AlemaniaFil: de los Campos, Gustavo. Michigan State University; Estados UnidosFil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; ArgentinaFil: Freudenthal, Jan. Universität Würzburg; AlemaniaFil: Korte, Arthur. Universität Würzburg; AlemaniaFil: Munilla Leguizamon, Sebastian. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Cátedra de Mejoramiento Genético Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Com o diabo no corpo: os terríveis papagaios do Brasil colônia

Desde a Antiguidade, papagaios, periquitos e afins (Psittacidae) fascinaram os europeus por seu vivo colorido e uma notável capacidade de interação com seres humanos. A descoberta do Novo Mundo nada faria além de acrescentar novos elementos ao tráfico de animais exóticos há muito estabelecido pelos europeus com a África e o Oriente. Sem possuir grandes mamíferos, a América tropical participaria desse comércio com o que tinha de mais atrativo, essencialmente felinos, primatas e aves - em particular os papagaios, os quais eram embarcados em bom número. Contudo, a julgar pelos documentos do Brasil colônia, esses voláteis podiam inspirar muito pouca simpatia, pois nenhum outro animal - exceto as formigas - foi tantas vezes mencionado como praga para a agricultura. Além disso, alguns psitácidas mostravam-se tão loquazes que inspiravam a séria desconfiança de serem animais demoníacos ou possessos, pois só três classes de entidades - anjos, homens e demônios - possuíam o dom da palavra. Nos dias de hoje, vários representantes dos Psittacidae ainda constituem uma ameaça para a agricultura, enquanto os indivíduos muito faladores continuam despertando a suspeita de estarem possuídos pelo demônio. Transcendendo a mera curiosidade, essa crença exemplifica o quão intrincadas podem ser as relações do homem com o chamado “mundo natural”, revelando um universo mais amplo e multifacetado do que se poderia supor a princípio. Nesse sentido, a existência de aves capazes de falar torna essa relação ainda mais complexa e evidencia que as dificuldades de estabelecer o limite entre o animal e o humano se estendem além dos primatas e envolvem as mais inusitadas espécies zoológicas.Since ancient times, parrots and their allies (Psittacidae) have fascinated Europeans by their striking colors and notable ability to interact with human beings. The discovery of the New World added new species to the international exotic animal trade, which for many centuries had brought beasts to Europe from Africa and the Orient. Lacking large mammals, tropical America participated in this trade with its most appealing species, essentially felines, primates and birds - especially parrots - which were shipped in large numbers. It should be noted, however, that at times these birds were not well liked. In fact, according to documents from colonial Brazil, only the ants rank higher than parrots as the animals most often mentioned as agricultural pests. On the other hand, some of these birds were so chatty that people suspected them to be demonic or possessed animals, since only three classes of beings - angels, men and demons - have the ability to speak. Nowadays, several Psittacidae still constitute a threat to agriculture, and the suspicion that extremely talkative birds were demon possessed has also survived. More than a joke or a mere curiosity, this belief exemplifies how intricate man’s relationships with the “natural world” may be. In this sense, the existence of birds that are able to speak adds a further twist to these relationships, demonstrating that the problem of establishing a boundary between the animal and the human does not only involve primates, but also includes some unusual zoological species

Hammerschmidova Historia Pragensis - in duas partes divisa

monografi

Ab Initio Study of the Structure of Guanine-Cytosine Base Pair Conformers in Gas Phase and Polar Solvents

The structure and energetics of the base pairing and proton transfer in the Watson-Crick type of guanine-cytosine base pair are studied by the HF/MINI-1 method within the full gradient optimization and self-consistent reaction field techniques. Two minima and the transition state on the connecting minimum energy path were located on the potential energy surface (PES) of this complex. The minima involved the canonical amino-keto base pair (GC) and the 4-iminocytosine-6-hydroxyguanine base pair (G*C*), which the latter being formed from GC by a simultaneous transfer of two protons in neighbouring hydrogen bonds. A polar environment was found to stabilize the canonical structure by 1·3 kcal mol-1 with respect to the rare tautomer G*C*. The GC pair represents the global minimum on the HF/MINI-1 PES in both gas phase and polar environment. The polar environment was also found to decrease the interaction enthalpy of the GC base pair and to influence significantly the geometry of the hydrogen bonds. The tautomeric origin of spontaneous point mutations and the recent observation of the different rotation rates about the cytosine and guanine amino bonds in the GC base pair are discussed