Transforming phylogenetic networks: Moving beyond tree space
Katharina T. Huber, Vincent Moulton, Taoyang Wu

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks.

Inferring population size history from large samples of genome wide molecular data – an approximate Bayesian computation approach

Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations

Quasispecies dynamics on a network of interacting genotypes and idiotypes: Applications to autoimmunity and immunodeficiency
Valmir C. Barbosa, Raul Donangelo, Sergio R. Souza

In spite of their many facets, the phenomena of autoimmunity and immunodeficiency seem to be related to each other through the subtle links connecting retroviral mutation and action to immune response and adaptation. In a previous work, we introduced a network model of how a set of interrelated genotypes (called a quasispecies, in the stationary state) and a set of interrelated idiotypes (an idiotypic network) interact. That model, which does not cover the case of a retroviral quasispecies, was instrumental for the study of quasispecies survival when confronting the immune system and led to the conclusion that, unlike what happens when a quasispecies is left to evolve by itself, letting genotypes mutate too infrequently leads to the destruction of the quasispecies. Here we extend that genotype-idiotype interaction model by the addition of a further parameter (ν) to account for the action of retroviruses (i.e., the destruction of idiotypes by genotypes). We give simulation results within a suitable parameter niche, highlighting the issues of quasispecies survival and of the onset of autoimmunity through the appearance of the so-called pathogenic idiotypes. Our main findings refer to how ν and λ, a parameter describing the rate at which idiotypes get stimulated, relate to each other. While for ν>λ the quasispecies survives at the expense of weakening the immune system significantly or even destroying it, for ν<λ the fittest genotypes of the quasispecies become mimicked inside the immune system as pathogenic idiotypes. The latter is in agreement with the current understanding of the HIV quasispecies.

Expanded Distance-based Phylogenetic Analyses of Fossil Homo Skull Shape Evolution
Peter J. Waddell

Analyses of a set of 47 fossil and 4 modern skulls using phylogenetic geometric morphometric methods corroborate and refine earlier results. These include evidence that the African Iwo Eleru skull, only about 12,000 years old, indeed represents a new species of near human. In contrast, the earliest known anatomically modern human skull, Qafzeh 9, the skull of Eve from Israel/Palestine, is validated as fully modern in form. Analyses clearly show evidence of archaic introgression into Gravettian, pre_Gravettian, Qafzeh, and Upper Cave (China) populations of near modern humans, and in about that order of increasing archaic content. The enigmatic Saldahna (Elandsfontein) skull emerges as a probable first representative of that lineage, which exclusive of Neanderthals that, eventually lead to modern humans. There is also evidence that the poorly dated Kabwe (Broken Hill) skull represents a much earlier distinct lineage. The clarity of the results bode well for quantitative statistical phylogenetic methods making significant inroads in the stalemates of paleoanthropology.