Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies

Free radicals – an evolutionary perspective

This chapter provides an evolutionary perspective on free radical biology. We first explain the concept of life history trade-offs and discuss how the need to manage oxidative stress in an optimal way may be an important mechanism driving the outcome of many of these trade-offs. We examine the different solutions that organisms have evolved to combat the damaging consequences of oxidative stress. We then examine the ways in which balancing investment in such defenses against the consequences of sustaining damage has influenced life history traits such in the context of growth, foraging, diet and activity patterns, sexual signaling, reproduction, and defense against infection