Several developments regarding the analysis of gene co-expression profiles using complex network theory have been reported recently. Such approaches usually start with the construction of an unweighted gene co-expression network, therefore requiring the selection of a suitable threshold defining which pairs of vertices will be connected. We aimed at addressing such an important problem by suggesting and comparing five different approaches for threshold selection. Each of the methods considers a respective biologically-motivated criterion for electing a potentially suitable threshold. A set of 21 microarray experiments from different biological groups was used to investigate the effect of applying the five proposed criteria to several biological situations. For each experiment, we used the Pearson correlation coefficient to measure the relationship between each gene pair, and the resulting weight matrices were thresholded considering several values, generating respective adjacency matrices (co-expression networks). Each of the five proposed criteria was then applied in order to select the respective threshold value. The effects of these thresholding approaches on the topology of the resulting networks were compared by using several measurements, and we verified that, depending on the database, the impact on the topological properties can be large. However, a group of databases was verified to be similarly affected by most of the considered criteria. Based on such results, it can be suggested that when the generated networks present similar measurements, the thresholding method can be chosen with greater freedom. If the generated networks are markedly different, the thresholding method that better suits the interests of each specific research study represents a reasonable choice.

Studies assessing the effects of the spatial distribution of ant nests on ant‐plant mutualisms are rare, even though they could be decisive to the outcomes of such interactions. Here, we investigated how ant nest abundance and richness affected a Neotropical plant with extrafloral nectaries (EFN), Smilax polyantha (Smilacaceae). We used baits to sample all nests of mutualistic ants within a 12 m radius of each plant. All neighbouring plants with EFN within 10 m of each tagged plant were also sampled. We measured foliar herbivory and fruit production of each S. polyantha. We hypothesized that (i) high numbers of ant nests near S. polyantha individuals would reduce foliar herbivory and increase fruit production, and that (ii) high ant nest richness would increase foliar herbivory and reduce fruit production. Results showed that plants surrounded by more ant nests had lower foliar herbivory and higher fruit production. However, ant nest richness was associated with higher foliar herbivory. Furthermore, plants producing more leaves and those surrounded by more neighbouring plants with EFN had reduced herbivory. Despite this, S. polyantha had low numbers of ant nests and reduced fruit production when surrounded by high numbers of neighbours with EFN. We suggest that the spatial distribution of ant nests and resources (plants with EFN) play an important role in ant‐mediated mutualisms, where both ants and plants are likely competing for each other's services. Thus, incorporating these two variables in ecological models should provide insights into how protective mutualisms are structured.

We described the geographic distribution of 82 haemosporidian lineages ( Plasmodium , Haemoproteus , and Leucocytozoon ) in the cattle egret sampled in five countries in central-western and southern Africa. Seventy-three lineages have not previously been reported. We determined the prevalence of three haemosporidians in the samples. We investigated the influence of the internal environment of the host and environmental variables on the Plasmodium diversity and whether environmental variables may explain spatial variations in the prevalence of Plasmodium . We screened DNA from 509 blood samples from nestlings in 15 African colonies for infection by sequencing the cytochrome b gene of parasites. The molecular phylogenetic analysis was performed using Bayesian methods and including sequences from the MalAvi and GeneBank databases. We found 62 new Plasmodium lineages in a clade with MYCAME02, which is a lineage described in waterbirds and recently identified in birds of prey as Plasmodium paranucleophilum . Two Haemoproteus lineages identified in cattle egret formed a distinct group with Haemoproteus catharti and MYCAMH1 ( Haemoproteus spp.). Seven Leucocytozoon lineages found in the cattle egret clustered with Leucocytozoon californicus . We found different Plasmodium diversities among the colonies sampled, demonstrating that the internal environment of the host is not the primary determinant of diversity. A linear mixed-effects multivariate model showed that precipitation was positively associated with Plasmodium diversity when controlling for the effects of temperature, colony composition (mixed and non-mixed species) and country. Moreover, a generalized mixed model showed that temperature was positively associated with the prevalence of Plasmodium when controlling for precipitation, elevation and country. We conclude that the cattle egret is a good model for future haemosporidian studies, as we found a significant number of new lineages in this host, which occupies regions with different climate characteristics where environmental variables exert an influence on the diversity and prevalence of Plasmodium .

ResumoUma das possíveis razões do sucesso da área de Redes Complexas decorre da flexibilidade destas estruturas para representação e modelagem de inúmeros sistemas complexos, incluindo em biologia. Entretanto, existem alguns aspectos do uso destes conceitos ainda pouco detalhados, como a questão da limiarização de relacionamentos graduados de forma a se obter uma rede binária de conexões. Uma outra questão interessante, ainda em aberto, refere-se a como redes complexas derivadas de sistemas diversos assemelham-se ou não umas às outras. Em biologia, esta questão aparece com particular interesse no que se refere às escalas das estruturas e sistemas biológicos, motivando a busca de analogias estruturais e funcionais. O presente trabalho de doutorado situa-se na interseção destes dois problemas. Em primeiro lugar, utilizamos a importante questão da limiarização de redes de co-expressão gênica como laboratório para desenvolver e comparar cinco métodos deste tipo, com fundamentações diferentes. Verificamos que dependendo da natureza do banco de dados, o impacto da limiarização nas propriedades topológicas pode ser grande, e sugerimos diretrizes de como utilizar os métodos diante do comportamento dos dados.Em seguida, abordamos a representação dos canais do sistema Haversiano dos ossos, com o objetivo de estudar este problema em particular e compará-lo com as redes de co-expressão na busca de analogias topológicas. As análises mostraram que os ossos são indistinguíveis em relação às propriedades topológicas das redes, mas nota-se uma variação mais pronunciada em relação às propriedades geométricas. Isso sugere que a arquitetura topológica do sistema vascular pode ser independente do tipo ósseo, mas que a demanda biológica de transporte pode variar em relação à posição no mesmo osso, e entre ossos diferentes.Como as redes do sistema Haversiano possuem pesos relacionados à espessura dos canais, utilizamos e comparamos os métodos de limiarização aqui propostos como forma de validação dos resultados. Concluindo estes desenvolvimentos, realizamos uma comparação estrutural dos dois tipos de redes obtidas, ou seja, de co-expressão gênica e de canais Haversianos. Palavras-chave: Redes Complexas, limiarização, limiar, expressão gênica, rede de co-expressão gênica, ossos, sistema Haversiano, canais de Havers, canais de Volkmann iv Abstract One of the possible reasons for the success of Complex Networks arises from the flexibility of these structures for representation and modeling of numerous complex systems, including in biology. However, there are still some aspects of the use of these concepts, such as the question of the thresholding of graduated relationships in order to obtain a binary network of connections. Another interesting question, still open, concerns how complex networks derived from different systems are similar to another or are not.In biology, this question appears with particular interest in the scales of biological structures and systems, motivating the search for structural and functional analogies. The prese...