A geography-aware reconciliation method to investigate diversification patterns in host/parasite interactions

Evoregions of fleas and their small mammalian hosts: Do they coincide?

Combining the biogeography and phylogenetic patterns of parasite-host associations allows a better understanding of the history of parasite–host interactions, which can be achieved via biogeographic regionalization incorporating phylogenetic information. Recently, the concepts of evoregions (regions where a majority of species evolved from one or several ancestors inhabiting these regions) and evolutionary transition zones (regions of high phylogenetic turnover) have been proposed, coupled with a classification approach for these concepts. We applied this approach to 206 flea species and 265 host species of the Palearctic and aimed to identify evoregions and evolutionary transition zones for both fleas and hosts and to understand whether these evoregions and transition zones match each other. We identified 5 evoregions with 3 transition zones for either fleas or hosts, but neither the positions and boundaries of the flea and host evoregions nor the transition zones coincided. Indications of multiple geographic centres of diversification of the same flea lineages suggested that (a) the common evolutionary history of fleas and hosts was characterized by multiple events other than codiversification and that (b) dispersal played an important role in flea and host assemblies. Barriers to dispersal could be represented by landscape features (deserts and mountain ranges) and/or climate differences.

Next-generation cophylogeny: unravelling eco-evolutionary processes

A fundamental question in evolutionary biology is how microevolutionary processes translate into species diversification. Cophylogeny provides an appropriate framework to address this for symbiotic associations, but historically has been primarily limited to unveiling patterns. We argue that it is essential to integrate advances from ecology and evolutionary biology into cophylogeny, to gain greater mechanistic insights and transform cophylogeny into a platform to advance understanding of interspecific interactions and diversification more widely. We discuss key directions, such as incorporating trait reconstruction and considering multiple scales of network organization, and highlight recent developments for implementation. A new quantitative framework is proposed to allow integration of relevant information, such as quantitative traits and assessment of the contribution of individual mechanisms to cophylogenetic patterns.

A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation

An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss, and mobilization patterns of the gene within the genomes in which it disseminates. In this article, we formalize this microbiological goal as a new pattern-matching problem in the domain of gene tree and species tree reconciliation, denoted "Reconciliation-Scenario Altering Mutation (RSAM) Discovery." We propose an [Formula: see text] time algorithm to solve this new problem, where m and n are the number of vertices of the input gene tree and species tree, respectively, and k is a user-specified parameter that bounds from above the number of optimal solutions of interest. The algorithm first constructs a hypergraph representing the k highest scoring reconciliation scenarios between the given gene tree and species tree, and then interrogates this hypergraph for subtrees matching a prespecified RSAM pattern. Our algorithm is optimal in the sense that the number of hypernodes in the hypergraph can be lower bounded by [Formula: see text]. We implement the new algorithm as a tool, called RSAM-finder, and demonstrate its application to the identification of RSAMs in toxins and drug resistance elements across a data set spanning hundreds of species.

Substrate-specificity of cytochrome P450-mediated detoxification as an evolutionary strategy for specialization on furanocoumarin-containing hostplants: CYP6AE89 in parsnip webworms

The parsnip webworm, Depressaria pastinacella, is restricted to two hostplant genera containing six structurally diverse furanocoumarins. Of these, imperatorin is detoxified by a specialized cytochrome P450, CYP6AB3. A previous whole-larva transcriptome analysis confirmed the presence of nine transcripts that belong to the CYP6AE subfamily. Here, by examining midgut-specific gene expression patterns we determined that CYP6AE89 transcripts were highly expressed and furanocoumarin-inducible. Computer docking and energy-minimization of a CYP6AE89 model with all six furanocoumarins showed that 5-methoxylated bergapten and 8-methoxylated xanthotoxin had the smallest distances from the heme to the proton-donor residue in the catalytic I-helix, and that the 5,8-dimethoxylated isopimpinellin and bergapten had the smallest energy-minimized distance from the heme oxygen to the furan ring double bond. To evaluate this prediction, we expressed the CYP6AE89 protein in an Escherichia coli system, and used it to detect high catalytic activity against the two mono-methoxylated linear furanocoumarins - bergapten and xanthotoxin - and weak activity against isopimpinellin. Thus, CYP6AE89, like CYP6AB3, is probably specialized for detoxifying only a subset of hostplant furanocoumarins. A maximum-likelihood tree built with six representative lepidopterans with manually annotated cytochrome P450s shows that CYP6AE89 may have evolved much faster than the other CYP6AE proteins, possibly indicative of host selection pressure.