Darwinian cultural evolution rivals genetic evolution

The study of culture from an evolutionary perspective has been slowed by resistance from some quarters of anthropology, a poor appreciation of the fidelity of cultural transmission, and misunderstandings about human intentionality.

Speciation as an active force in promoting genetic evolution

There is a growing appreciation among evolutionary biologists that the rate and tempo of molecular evolution might often be altered at or near the time of speciation, i.e. that speciation is in some way a special time for genes. Molecular phylogenies frequently reveal increased rates of genetic evolution associated with speciation and other lines of investigation suggest that various types of abrupt genomic disruption can play an important role in promoting speciation via reproductive isolation. These phenomena are in conflict with the gradual view of molecular evolution that is implicit in much of our thinking about speciation and in the tools of modern biology. This raises the prospect of studying the molecular evolutionary consequences of speciation per se and studying the footprint of speciation as an active force in promoting genetic divergence. Here we discuss the reasons to believe that speciation can play such a role and elaborate on possible mechanisms for accelerated rates of evolution following speciation. We provide an example of how it is possible detect whether accelerated bursts of evolution occur in neutral and/or adaptive regions of genes and discuss the implications of rapid episodes of change for conventional models of molecular evolution. Speciation might often owe more to ephemeral and essentially arbitrary events that cause reproductive isolation than to the gradual and regular tug of natural selection that draws a species into a new niche.

Molecular epidemiology and evolution of avian infectious bronchitis virus

Mutation and recombination processes are involved in the genetic and phenotypic variations of RNA viruses, leading to the emergence of new variant strains, and give rise to virus population diversity to be modeled by the host, particularly by the immune system, as occurred with infectious bronchitis virus (IBV) in chickens. The consequence is a continuous emergence of new IBV variants with regard to pathotypes, serotypes, and protectotypes. Nucleotide sequencing and subsequent genetic analysis of the S1 and N protein gene sequences provide a fast and accurate method to classify and predict IBV genotype, and a powerful instrument to monitor phylogenetic and epidemiological evolution of IBV variants. Despite the use of vaccination programmes, infectious bronchitis has become a serious problem in Brazil. Thus, a significant number of IBV field variants have been identified circulating in the Brazilian commercial poultries between 2000 to 2006 and more recently in Argentina. These viruses seem to be indigenous, because they demonstrated a low genetic relatedness with the majority of the reference strains from North America, Europe and Asia, but were moderately to highly related one to another. In summary, indigenous field IBV variants were evolving and circulating in the field in Brazil and Argentina, and should be considered as initial candidates for protection against current IBV infectious in chickens. However, in vitro and in vivo studies are needed to determine the pathogenicity and immunogenecity of these new isolates, before defining a new vaccine strain.

Three linked enzyme loci in fishes: implications in the evolution of vertebrate chromosomes.

A three-point linkage group comprised of loci coding for adenosine deaminase (ADA), glucose-6-phosphate dehydrogenase (G6PDH), and 6-phospho-gluconate dehydrogenase (6PGD) is described in fish of the genus Xiphophorus (Poeciliidae). The alleles at loci in this group were shown to assort independently from the alleles at three other loci--isocitrate dehydrogenase 1 and 2, and glyceraldehyde-3-phosphate dehydrogenase 1. Alleles at the latter three loci also assort independently from each other. Data were obtained by observing the segregation of electrophoretically variant alleles in reciprocal backcross hybrids derived from crosses between either X. helleri guentheri or X. h. strigatus and X. maculatus. The linkage component of chi2 was significant (less than 0.01) in all crosses, indicating that the linkage group is conserved in all populations of both species of Xiphophorus examined. While data from X. h. guentheri backcrosses indicate the linkage relationship ADA--6%--G6PDH--24%--6PGD, and ADA--29%--6PGD (30% when corrected for double crossovers), data from backcrosses involving strigatus, while supporting the same gene order, yielded significantly different recombination frequencies. The likelihood of the difference being due to an inversion could not be separated from the possibility of a sex effect on recombination in the present data. The linkage of 6PGD and G6PDH has been shown to exist in species of at least three classes of vertebrates, indicating the possibility of evolutionary conservation of this linkage.

Optimal ground control points for geometric correction using genetic algorithm with glboal accuracy

Establishing the ground control point (GCP) network is a pre-requisite for georeferencing raw image data. Given current typical digital spatial database quality, much interest among users is about the accuracy of the geometric correction model that yields the final product. This paper reports an approach to optimizing GCP assembly using a genetic/evolution algorithm. The paper also suggests an optimal criterion for accuracy assessment through appraisal of global accuracy of the transformation, which is computed at each point of the image space. Experimental results demonstrate that the proposed approach has a great potential for selection of the best GCPs, and considerable improvement to the accuracy of geometric correction models can be expected when it is implemented.

均衡重力异常计算与综合解释——以黄海地区为例

Petroleum and Natural Gas is an important strategic resources. The reserves of Petroleum and Natural Gas can’t meet the need of our country, which also blocks the development of economy and threatens the safety of national. Therefore, it makes a great sense to bring “the second round of oil & gas exploration” into effect and study the exploration of oil and gas of Pre-Cenozoic residual basins in China. The integrated geophysical exploration is the main way to research the Pre-Cenozoic residual basins. Gravity exploration is one of the most important exploration methods, which has played an important role in oil and gas prospecting, such as compartmentalizing geotectonic elements, delineating the distribution range of sedimentary basins, searching oil and gas structure, abstracting oil and gas information, and so on, from its naissance. The isostatic gravity anomalies is significant for exploration, which can help us research deep crustal structure, the equilibrium state of earth, the geologic structure of shallow crust, the basement shape of sedimentary basins and the genetic evolution of sedimentary basins. In the paper, we stress the implication and physical meanings systemically, and discuss the calculation theory. On the basis of previous work, we test different isostatic compensation models and parameters to find out their influences to the result of isostatic gravity anomalies. In addition, we improve the method of isostatic gravity anomalies calculation and give a system of isostatic gravity anomalies calculation which is proved has satisfying effect. From the research above, we find that the results of Platt model and Airy model are consistent, which have similar form and almost the same value. However, by contrast, the Airy model is proved has better adaptability than Platt model. The two main parameters——crust thickness and density difference of crust and mantle, both have influence to the isostatic gravity anomalies, but the latter have more. Finally, we adopt the regional field extending edge method to make the result more of actual geologic condition. On the methods above, we calculate the isostatic gravity anomalies field in Yellow Sea area from the Bouguer gravity anomalies and the water depth and altitude data. And then the isostatic gravity anomalies character is analyzed and the integrated geological-geophysical interpretation is made on the basis of summarizing the previous research result systemically and analyzing other geophysical data and geological information. From the research, we find that the Yellow Sea area belongs to continental type crust equilibrium regions, where the isostatic gravity anomalies field is placid and has less fluctuation values, which implies that the area is in equilibrium state to different extends.

Identification et caractérisation génétique et phénotypique de deux espèces de Cryptosporidium après divers passages chez le veau

L’étude de la variation du génotype et du phénotype fut réalisée sur deux espèces de parasites intestinaux (Cryptosporidium parvum et C. muris) via une infection expérimentale de 10 passages successifs chez le veau (Bos taurus). L’infection avec C. parvum a bien fonctionné alors qu’aucun signe clinique n’a été observé dans le cadre de cette étude avec C. muris. Pour le génotype, deux gènes (HSP70 et GP60) ont été amplifiés par double PCR puis séquencés. Les résultats ont indiqué que ces gènes n’étaient pas modifiés après 10 passages chez des veaux. Cela montre une faible évolution génétique du parasite lorsqu’il passe dans un animal hôte, facilitant ainsi les études épidémiologiques lors d’épisode de cryptosporidiose. Il faut cependant noter que les parasites utilisés ne provenaient pas de l’environnement mais d’une compagnie spécialisée en parasitologie (WaterBorne®). L’étude de la variation du phénotype a été tentée, sans succès, à l’aide d’un immuno-buvardage en point utilisant le sérum des veaux infectés. Des problèmes liés à la concentration des ookystes de C. parvum placés sur la membrane de l’immuno-buvardage en point furent suspectés.

Étude de l’évolution du tropisme et de la pression sélective exercée sur le gène de l’enveloppe du virus de l’immunodéficience humaine de type 1 au cours de la grossesse et à l’échelle de la population.

Introduction. Le VIH-1 évolue en fonction de la réponse immunitaire spécifique de l’hôte. La pression sélective exercée par la réponse immunitaire VIH-spécifique de l’hôte entraine l’évolution des gènes viraux et à terme détermine l’évolution de la maladie. Cette évolution du virus à l’échelle d’un individu façonne également l’évolution du virus à l’échelle de la population et détermine le devenir de l’épidémie. Le VIH utilise les corécepteurs d’entrée CCR5 (virus R5) et CXCR4 (virus X4) afin d’infecter la cellule cible, et l’évolution du tropisme du virus de R5 vers X4, appelé switch du tropisme, est associé à la progression de la maladie. Les virus R5 sont rencontrés en début d’infection tandis que les virus X4 apparaissent en fin de maladie chez un certain de nombre de patients et sont considérés comme plus virulents. La pression sélective immunitaire exercée sur le gène de l’enveloppe (env) peut donc entrainer l’évolution du tropisme du VIH. La grossesse est un état immunitaire particulier considéré comme étant principalement caractérisé par un biais Th2 nécessaire à l’établissement de la tolérance materno-fétale. Le switch de tropisme de R5 vers X4 en grossesse n’a jamais été documenté, de même que l’évolution des déterminants du tropisme à l’échelle de la population. Hypothèses. Les changements immunitaires associés à l’initiation et la progression de la grossesse engendrent des changements dans la pression immunitaire exercée sur l’enveloppe et peuvent favoriser le switch du tropisme. L’évolution du tropisme du VIH-1 peut être observé à l’échelle de la population au même titre que l’évolution de l’enveloppe virale. Objectifs. Analyser l’évolution du tropisme et décrire la pression sélective sur l’enveloppe des femmes enceintes infectées par le VIH-1. Analyser l’évolution des déterminants du tropisme à l’échelle de la population. Méthodes. Nous avons dans un premier temps analysé l’évolution des déterminants du tropisme et déterminé le génotype et phénotype du VIH-1 chez 19 femmes enceintes issues de la cohorte du centre maternel et infantile sur le SIDA de l’hôpital Sainte-Justine (CMIS). Nous avons ensuite caractérisé et comparé la pression sélective exercée sur env, par une méthode bayésienne, chez 31 femmes enceinte et 29 femmes non-enceintes. Enfin, nous avons analysé et comparé des déterminants du tropisme entre des séquences d’enveloppe contemporaines et anciennes, issues des bases de données du NCBI. Résultats. Nos résultats montrent la présence de virus X4 chez la moitié de notre cohorte, et un switch de tropisme de R5 vers X4 chez 5/19 sujets. Les séquences des femmes enceintes présentaient des taux de substitutions plus élevées que celles des femmes non-enceintes. La pression sélective dans la région C2 était plus faible chez les femmes enceintes que chez les femmes non-enceintes, et différait dans 4 positions entre ces 2 groupes. Cette sélection diminuait au cours de la grossesse chez les patientes traitées. Enfin, une accumulation de mutations X4 a été observée dans les séquences R5 contemporaines par rapport aux séquences R5 anciennes. Conclusion. Les changements immunitaires associés à la grossesse semblent induire des modifications subtiles dans la pression sélective exercée sur env, suffisant à influencer l’évolution du tropisme de R5 vers X4. Un switch du tropisme à l’échelle de la population impliquerait une épidémie évoluant vers une plus grande virulence du virus. Nos résultats sont d’importance en ce qui concerne la prophylaxie antirétrovirale pour la santé de la mère et la prévention de la transmission mère-enfant du VIH-1. Ils sont aussi importants concernant l’avenir de la thérapie antirétrovirale dans le contexte d’une épidémie évoluant vers une plus grande virulence

Parâmetros genéticos para idade ao primeiro parto estimados por diferentes modelos para rebanhos da raça Nelore

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

Overview on the performance of Brazilian broilers (1990 to 2009)

This article describes the genetic evolution of commercial broilers between 1990 and 2009, considering live performance, in particular, in terms of weight gain and feed conversion ratio. In order to determine if the assumption that the relationship between body weight gain and feed conversion ratio is increasing and positive, information on all broiler strains reared in Brazil were collected from several companies present in five Brazilian regions. This survey aimed at evaluating broiler live performance as a function of genetic improvement with time. Broiler performance improved, as shown by the statistical differences obtained for the following parameters: livability, live weight, daily weight gain, feed conversion ratio, and production efficiency index between 1990 and 2009. However, live weight gain and feed conversion ratio are emphasized due to the significant differences found along the studied period.

Perfil genotípico de resistência do vírus Influenza A (H1N1) pandêmico aos inibidores da neuraminidase em pacientes procedentes da mesorregião de Belém no período de maio de 2009 a maio de 2012

O vírus Influenza é o responsável pela gripe, uma doença que ocasiona milhões de mortes e hospitalizações todos os anos. Nas infecções severas, especialmente em pessoas com risco para complicações, os antivirais tornam-se os principais meios para o manejo clínico, merecendo especial destaque os inibidores da neuraminidase (INAs). De fato, na pandemia de 2009 a Organização Mundial da Saúde (OMS) recomendou o uso do oseltamivir para o tratamento dos doentes. Porém, devido à evolução genética viral, surgiram cepas com mutações no gene codificador da neuraminidase (NA) responsáveis por substituições aminoacídicas que levam à resistência aos fármacos INAs. Assim, a OMS passou a recomendar a vigilância de resistência genotípica para os vírus Influenza. Este trabalho teve como objetivos verificar a ocorrência de mutações no gene codificador da NA dos vírus Influenza A (H1N1) pandêmico que possam estar relacionadas à resistência aos INAs em cepas circulantes na mesorregião metropolitana de Belém no período de maio de 2009 a maio de 2012 e analisar, através da modelagem de proteínas, as substituições aminoacídicas da NA que possam estar influenciando na conformação protéica. Durante o período de estudo, foram recebidas no Laboratório de Vírus Respiratórios 2619 amostras clínicas de pacientes que apresentavam sinais e sintomas de infecção respiratória aguda com até cinco dias de evolução. Para a detecção do genoma viral foi feita a extração do RNA viral, seguida de RT-PCR em tempo real utilizando marcadores específicos para Influenza A H1N1pdm, resultando em 744 (28,4%) positivas. Parte das amostras positivas foram então inoculadas em células MDCK. Para as amostras isoladas em cultura de células, foi feita uma nova extração do RNA viral seguida de uma RT-PCR e semi-nested (PCR) utilizando iniciadores específicos para o gene NA, e posterior análise em sequenciador automático ABI Prism 3130xl (Applied Biosystems). A modelagem molecular da NA foi realizada através dos softwares SWISS-MODEL, MODELLER 9.10, PROCHECK, VERIFY3D e PYMOL. A análise parcial das sequências da neuraminidase nas amostras sequenciadas mostrou que não houve a circulação de cepas de vírus H1N1pdm com a mutação H275Y, a principal envolvida na resistência ao oseltamivir. Porém, em duas amostras foi identificada a substituição D199N que já foi relatada em vários estudos mostrando uma possível associação com o aumento da resistência ao oseltamivir. As amostras de 2012 apresentaram duas substituições (V241I e N369K) que estão relacionadas com um possível papel na compensação dos efeitos negativos causados pela mutação H275Y. A modelagem molecular mostrou que na mutação D199N houve uma alteração na estrutura da proteína NA próxima ao sítio de ligação ao antiviral. A análise filogenética revelou que as amostras de 2012 formaram um cluster isolado, demonstrando uma variação muito mais temporal do que geográfica. Este representa o primeiro estudo de resistência dos vírus Influenza H1N1pdm na mesorregião metropolitana de Belém, representando um importante instrumento para que os profissionais de saúde adotem estratégias mais eficazes no manejo da doença e no desenvolvimento de novos fármacos anti-influenza.

Logística operacional: alocação de bases operacionais em distribuição de energia elétrica.

Ser eficiente é um requisito para a sustentabilidade das empresas concessionárias de distribuição de energia elétrica no Brasil. A busca pela eficiência deve estar em harmonia com a melhoria contínua da qualidade, da segurança e da satisfação dos consumidores e das partes envolvidas. O desafio de atender múltiplos objetivos requer que as empresas do setor desenvolvam soluções inovadoras, com a mudança de processos, tecnologia, estrutura e a capacitação das pessoas. Desenvolver um modelo operacional eficiente e uma gestão rigorosa dos custos são fatores-chave para o sucesso das empresas, considerando o contexto regulatório de revisão tarifária que incentiva a melhoria do desempenho. O modelo operacional é definido a partir da organização logística dos recursos para atendimento da demanda de serviços, que define também os custos fixos e variáveis de pessoal (salário, horas extras, refeições), infraestrutura (manutenção de prédios, ferramentas e equipamentos) e deslocamentos (manutenção de veículos, combustível), por exemplo. A melhor alocação e o melhor dimensionamento de bases operacionais possibilitam a redução dos custos com deslocamento e infraestrutura, favorecendo o aproveitamento da força de trabalho em campo, a melhoria do atendimento dos clientes e da segurança dos colaboradores. Este trabalho apresenta uma metodologia de otimização de custos através da alocação de bases e equipes operacionais, com o modelamento matemático dos objetivos e restrições do negócio e a aplicação de algoritmo evolutivo para busca das melhores soluções, sendo uma aplicação de Pesquisa Operacional, no campo da Localização de Instalações, em distribuição de energia elétrica. O modelo de otimização desenvolvido possibilita a busca pelo ponto de equilíbrio ótimo que minimiza o custo total formado pelos custos de infraestrutura, frota (veículos e deslocamentos) e pessoal. O algoritmo evolutivo aplicado no modelo oferece soluções otimizadas pelo melhoramento de conjuntos de variáveis binárias com base em conceitos da evolução genética. O modelo de otimização fornece o detalhamento de toda a estrutura operacional e de custos para uma determinada solução do problema, utilizando premissas de produtividade e deslocamentos (velocidades e distâncias) para definir as abrangências de atuação das bases operacionais, recursos (equipes, pessoas, veículos) necessários para atendimento da demanda de serviços, e projetar todos os custos fixos e variáveis associados. A metodologia desenvolvida neste trabalho considera também a projeção de demanda futura para a aplicação no estudo de caso, que evidenciou a efetividade da metodologia como ferramenta para a melhoria da eficiência operacional em empresas de distribuição de energia elétrica.

Guiding Monte Carlo tree searches with neural networks in the game of go

A dissertation submitted in fulfillment of the requirements to the degree of Master in Computer Science and Computer Engineering

Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

trans gene regulation in adaptive evolution: A genetic algorithm model

This is a continuation of earlier studies on the evolution of infinite populations of haploid genotypes within a genetic algorithm framework. We had previously explored the evolutionary consequences of the existence of indeterminate—“plastic”—loci, where a plastic locus had a finite probability in each generation of functioning (being switched “on”) or not functioning (being switched “off”). The relative probabilities of the two outcomes were assigned on a stochastic basis. The present paper examines what happens when the transition probabilities are biased by the presence of regulatory genes. We find that under certain conditions regulatory genes can improve the adaptation of the population and speed up the rate of evolution (on occasion at the cost of lowering the degree of adaptation). Also, the existence of regulatory loci potentiates selection in favour of plasticity. There is a synergistic effect of regulatory genes on plastic alleles: the frequency of such alleles increases when regulatory loci are present. Thus, phenotypic selection alone can be a potentiating factor in a favour of better adaptation.