Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study

We study two problems in computational phylogenetics. The first is tree compatibility. The input is a collection of phylogenetic trees over different partially-overlapping sets of species. The goal is to find a single phylogenetic tree that displays all the evolutionary relationships implied by . The second problem is incomplete directed perfect phylogeny (IDPP). The input is a data matrix describing a collection of species by a set of characters, where some of the information is missing. The question is whether there exists a way to fill in the missing information so that the resulting matrix can be explained by a phylogenetic tree satisfying certain conditions. We explain the connection between tree compatibility and IDPP and show that a recent tree compatibility algorithm is effectively a generalization of an earlier IDPP algorithm. Both algorithms rely heavily on maintaining the connected components of a graph under a sequence of edge and vertex deletions, for which they use the dynamic connectivity data structure of Holm et al., known as HDT. We present a computational study of algorithms for tree compatibility and IDPP. We show experimentally that substituting HDT by a much simpler data structure—essentially, a single-level version of HDT—improves the performance of both of these algorithm in practice. We give partial empirical and theoretical justifications for this observation.

Observational and experimental evaluation of hemiparasite resistance in trees in the urban afforestation of Santarém, Pará, Brazil

ABSTRACT One of the problems affecting the quality of urban trees is their infestation by mistletoes (aerial hemiparasite plants of the order Santalales). Identification of the main types of trees infested, and of the causes of infestation patterns, can help infestation control and the planning of efficient planting regimes. In this sense, the aim of this study was to evaluate the patterns of hemiparasite infestation in trees in an Amazonian urban environment. We aimed to answer (1) which species of mistletoes occur on urban trees in the city of Santarém, in the Brazilian Amazon; (2) what is the proportion and intensity of infestation on infected trees; and (3) if differences in infestation rates among tree species can be explained by mistletoe-tree compatibility. We assessed mistletoe incidence and intensity of infestation on trees in the main avenues of the city. To evaluate the role of mistletoe-tree compatibility in the observed parasitism patterns, we carried out a seed inoculation experiment with seeds of the most abundant mistletoe, Passovia theloneura. Seeds were planted on three tree species (Andira inermis, Handroanthus serratifolius, and Mangifera indica). The overall infestation rate was 19.3%, with exotic tree species more infested than natives. The experiment showed that incompatibility between P. theloneura and the native H. serratifolius is primarily responsible for the observed non-infestation. Mistletoes germinated on A. inermis grew better than those on M. indica, contrary to the infestation prevalence found in the field, suggesting that patterns of infestation are also influenced by seed deposition processes.