Jane: a new tool for the cophylogeny reconstruction problem

<p>Abstract</p> <p>Background</p> <p>This paper describes the theory and implementation of a new software tool, called <it>Jane</it>, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new <it>Jane </it>tool described here provides functionality that complements existing tools.</p> <p>Results</p> <p>The <it>Jane </it>software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. <it>Jane </it>also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program.</p> <p>Conclusions</p> <p><it>Jane </it>is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.</p

The Cophylogeny Reconstruction Problem is NP-Complete

The cophylogeny reconstruction problem arises in the study of host-parasite relationships. Specif- ically, we are given a host tree H, a parasite tree P, and a function \u27 mapping the leaves (extant taxa) of P to the leaves of H. Four biologically plausible operations are considered: cospeciation, duplication, host switching, and loss (Figure 1). A host switch is permitted in conjunction with a duplication event but not with a cospeciation event [1]

Jane: A New Tool for the Cophylogeny Reconstruction Problem

Background This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools. Results The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program. Conclusions Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic M&#xfc;llerian mimicry, thought &#x2013; but rarely demonstrated &#x2013; to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of _H. erato_ and _H. melpomene_, supporting repeated codivergence of mimetic populations. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of _H. erato_ and _H. melpomene_ occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. This evidence supports a history of reciprocal coevolution between M&#xfc;llerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While duplication–loss (DL) reconciliation leads to a unique maximum-parsimony solution, duplication-transfer-loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult to infer the true evolutionary history of the gene family. This problem is further exacerbated by the fact that different event cost assignments yield different sets of optimal reconciliations. Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We show that even gene trees with only a few dozen genes often have millions of optimal reconciliations and present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn[superscript 2]) time per sample, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mappings and event assignments and to investigate the impact of varying event costs. We apply our method to a biological dataset of approximately 4700 gene trees from 100 taxa and observe that 93% of event assignments and 73% of mappings remain consistent across different multiple optima. Our analysis represents the first systematic investigation of the space of optimal DTL reconciliations and has many important implications for the study of gene family evolution.National Science Foundation (U.S.) (CAREER Award 0644282)National Institutes of Health (U.S.) (Grant RC2 HG005639)National Science Foundation (U.S.). Assembling the Tree of Life (Program) (Grant 0936234

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction

Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro‐evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host–parasite cophylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro‐evolutionary regime showed a low diversification rate, high frequency of duplication events and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics

Deciphering the origin and evolution of Hepatitis B viruses by means of a family of non-enveloped fish viruses

Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome organization with extensive gene overlap. Remarkably, the ∼1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of HBVs including genome replication via protein-primed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction indicates that these two virus families separated more than 400 million years ago before the rise of tetrapods. We show that HBVs are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo, leading to a major transition in viral lifestyle, followed by co-evolution with their hosts over geologic eras

An extreme case of plant-insect co-diversification: figs and fig-pollinating wasps

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale co-phylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on average, wasps had sequences from 77% of six genes (5.6kb), figs had sequences from 60% of five genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based co-phylogenetic analyses further support the co-diversification hypothesis. Biogeographic analyses indicate that the presentday distribution of fig and pollinator lineages is consistent with an Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term co-diversification