Leo van Iersel

Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest

Over the past two decades, several fungal outbreaks have occurred, including the high-profile ‘Vancouver Island’ and ‘Pacific Northwest’ outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of the tropical and subtropical climate zones where the species normally occurs. In every case, the causative agent belongs to a previously rare genotype of C. gattii called AFLP6/VGII, but the origin of the outbreak clades remains enigmatic. Here we used phylogenetic and recombination analyses, based on AFLP and multiple MLST datasets, and coalescence gene genealogy to demonstrate that these outbreaks have arisen from a highly-recombining C. gattii population in the native rainforest of Northern Brazil. Thus the modern virulent C. gattii AFLP6/VGII outbreak lineages derived from mating events in South America and then dispersed to temperate regions where they cause serious infections in humans and animals.

Networks: expanding evolutionary thinking

Networks allow the investigation of evolutionary relationships that do not fit a tree model. They are becoming a leading tool for describing the evolutionary relationships between organisms, given the comparative complexities among genomes.

Phylogenetic networks do not need to be complex

Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all clusters of such a dataset cannot be combined into a single phylogenetic tree. Phylogenetic networks are a generalization of phylogenetic trees that can be used to display more complex evolutionary histories, including reticulate events, such as hybridizations, recombinations and horizontal gene transfers. Here, we present the new Cass algorithm that can combine any set of clusters into a phylogenetic network. We show that the networks constructed by Cass are usually simpler than networks constructed by other available methods. Moreover, we show that Cass is guaranteed to produce a network with at most two reticulations per biconnected component, whenever such a network exists. We have implemented Cass and integrated it into the freely available Dendroscope software. Contact: l.j.j.v.iersel@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Geographically Structured Populations of Cryptococcus neoformans Variety grubii in Asia Correlate with HIV Status and Show a Clonal Population Structure

Cryptococcosis is an important fungal disease in Asia with an estimated 140,000 new infections annually the majority of which occurs in patients suffering from HIV/AIDS. Cryptococcus neoformans variety grubii (serotype A) is the major causative agent of this disease. In the present study, multilocus sequence typing (MLST) using the ISHAM MLST consensus scheme for the C. neoformans/C. gattii species complex was used to analyse nucleotide polymorphisms among 476 isolates of this pathogen obtained from 8 Asian countries. Population genetic analysis showed that the Asian C. neoformans var. grubii population shows limited genetic diversity and demonstrates a largely clonal mode of reproduction when compared with the global MLST dataset. HIV-status, sequence types and geography were found to be confounded. However, a correlation between sequence types and isolates from HIV-negative patients was observed among the Asian isolates. Observations of high gene flow between the Middle Eastern and the Southeastern Asian populations suggest that immigrant workers in the Middle East were originally infected in Southeastern Asia.

A quadratic kernel for computing the hybridization number of multiple trees

It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter tractable if an instance of the problem consists of precisely two such trees. In this paper, we show that this problem remains fixed-parameter tractable for an arbitrarily large set of rooted binary phylogenetic trees. In particular, we present a quadratic kernel.

How much information is needed to infer reticulate evolutionary histories

Phylogenetic networks are a generalization of evolutionary trees and are an important tool for analyzing reticulate evolutionary histories. Recently, there has been great interest in developing new methods to construct rooted phylogenetic networks, that is, networks whose internal vertices correspond to hypothetical ancestors, whose leaves correspond to sampled taxa, and in which vertices with more than one parent correspond to taxa formed by reticulate evolutionary events such as recombination or hybridization. Several methods for constructing evolutionary trees use the strategy of building up a tree from simpler building blocks (such as triplets or clusters), and so it is natural to look for ways to construct networks from smaller networks. In this article, we shall demonstrate a fundamental issue with this approach. Namely, we show that even if we are given all of the subnetworks induced on all proper subsets of the leaves of some rooted phylogenetic network, we still do not have all of the information required to completely determine that network. This implies that even if all of the building blocks for some reticulate evolutionary history were to be taken as the input for any given network building method, the method might still output an incorrect history. We also discuss some potential consequences of this result for constructing phylogenetic networks.

Trinets encode tree-child and level-2 phylogenetic networks

Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that

Nonbinary Tree-Based Phylogenetic Networks

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