Traversing the tangle: algorithms and applications for cophylogenetic studies

Wolbachia Interactions with Diverse Insect Hosts: From Reproductive Modulations to Sustainable Pest Management Strategies

Effective in a variety of insect orders, including dipteran, lepidopteran, and hemipteran, Wolbachia-based control tactics are investigated, noting the importance of sterile and incompatible insect techniques. Encouraging approaches for controlling Aedes mosquitoes are necessary, as demonstrated by the evaluation of a new SIT/IIT combination and the incorporation of SIT into Drosophila suzukii management. For example, Wolbachia may protect plants from rice pests, demonstrating its potential for agricultural biological vector management. Maternal transmission and cytoplasmic incompatibility dynamics are explored, while Wolbachia phenotypic impacts on mosquito and rice pest management are examined. The importance of host evolutionary distance is emphasised in recent scale insect research that addresses host-shifting. Using greater information, a suggested method for comprehending Wolbachia host variations in various contexts emphasises ecological connectivity. Endosymbionts passed on maternally in nematodes and arthropods, Wolbachia are widely distributed around the world and have evolved both mutualistic and parasitic traits. Wolbachia is positioned as a paradigm for microbial symbiosis due to advancements in multiomics, gene functional assays, and its effect on human health. The challenges and opportunities facing Wolbachia research include scale issues, ecological implications, ethical conundrums, and the possibility of customising strains through genetic engineering. It is thought that cooperative efforts are required to include Wolbachia-based therapies into pest management techniques while ensuring responsible and sustainable ways.

Geography, phylogeny and host switch drive the coevolution of parasitic Gyrodactylus flatworms and their hosts

BACKGROUND

Gyrodactylus is a lineage of monogenean flatworm ectoparasites exhibiting many features that make them a suitable model to study the host-parasite coevolutionary dynamics. Previous coevolutionary studies of this lineage mainly relied on low-power datasets (a small number of samples and a single molecular marker) and (now) outdated algorithms.

METHODS

To investigate the coevolutionary relationship of gyrodactylids and their fish hosts in high resolution, we used complete mitogenomes (including two newly sequenced Gyrodactylus species), a large number of species in the single-gene dataset, and four different coevolutionary algorithms.

RESULTS

The overall coevolutionary fit between the parasites and hosts was consistently significant. Multiple indicators confirmed that gyrodactylids are generally highly host-specific parasites, but several species could parasitize either multiple (more than 5) or phylogenetically distant fish hosts. The molecular dating results indicated that gyrodactylids tend to evolve towards high host specificity. Speciation by host switch was identified as a more important speciation mode than co-speciation. Assuming that the ancestral host belonged to Cypriniformes, we inferred four major host switch events to non-Cypriniformes hosts (mostly Salmoniformes), all of which occurred deep in the evolutionary history. Despite their relative rarity, these events had strong macroevolutionary consequences for gyrodactylid diversity. For example, in our dataset, 57.28% of all studied gyrodactylids parasitized only non-Cypriniformes hosts, which implies that the evolutionary history of more than half of all included lineages could be traced back to these major host switch events. The geographical co-occurrence of fishes and gyrodactylids determined the host use by these gyrodactylids, and geography accounted for most of the phylogenetic signal in host use.

CONCLUSIONS

Our findings suggest that the coevolution of Gyrodactylus flatworms and their hosts is largely driven by geography, phylogeny, and host switches.

Host phylogeny and ecological associations best explain Wolbachia host shifts in scale insects

Wolbachia are among the most prevalent and widespread endosymbiotic bacteria on Earth. Wolbachia's success in infecting an enormous number of arthropod species is attributed to two features: the range of phenotypes they induce in their hosts, and their ability to switch between host species. Whilst much progress has been made in elucidating their induced phenotypes, our understanding of Wolbachia host-shifting is still very limited: we lack answers to even fundamental questions concerning Wolbachia's routes of transfer and the importance of factors influencing host shifts. Here, we investigate the diversity and host-shift patterns of Wolbachia in scale insects, a group of arthropods with intimate associations with other insects that make them well suited to studying host shifts. Using Illumina multitarget amplicon sequencing of Wolbachia-infected scale insects and their direct associates we determined the identity of all Wolbachia strains. We then fitted a generalized additive mixed model to our data to estimate the influence of host phylogeny and the geographical distribution on Wolbachia strain sharing among scale insect species. The model predicts no significant contribution of host geography but strong effects of host phylogeny, with high rates of Wolbachia sharing among closely related species and a sudden drop-off in sharing with increasing phylogenetic distance. We also detected the same Wolbachia strain in scale insects and several intimately associated species (ants, wasps and flies). This indicates putative host shifts and potential routes of transfers via these associates and highlights the importance of ecological connectivity in Wolbachia host-shifting.

Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids

The study of congruency between phylogenies of interacting species can provide a powerful approach for understanding the evolutionary history of symbiotic associations. Orchid mycorrhizal fungi can survive independently of orchids making cospeciation unlikely, leading us to predict that any congruence would arise from host-switches to closely related fungal species. The Australasian orchid subtribe Drakaeinae is an iconic group of sexually deceptive orchids that consists of approximately 66 species. In this study, we investigated the evolutionary relationships between representatives of all six Drakaeinae orchid genera (39 species) and their mycorrhizal fungi. We used an exome capture dataset to generate the first well-resolved phylogeny of the Drakaeinae genera. A total of 10 closely related Tulasnella Operational Taxonomic Units (OTUs) and previously described species were associated with the Drakaeinae orchids. Three of them were shared among orchid genera, with each genus associating with 1-6 Tulasnella lineages. Cophylogenetic analyses show Drakaeinae orchids and their Tulasnella associates exhibit significant congruence (p < 0.001) in the topology of their phylogenetic trees. An event-based method also revealed significant congruence in Drakaeinae-Tulasnella relationships, with duplications (35), losses (25), and failure to diverge (9) the most frequent events, with minimal evidence for cospeciation (1) and host-switches (2). The high number of duplications suggests that the orchids speciate independently from the fungi, and the fungal species association of the ancestral orchid species is typically maintained in the daughter species. For the Drakaeinae-Tulasnella interaction, a pattern of phylogenetic niche conservatism rather than coevolution likely explains the observed phylogenetic congruency in orchid and fungal phylogenies. Given that many orchid genera are characterized by sharing of fungal species between closely related orchid species, we predict that these findings may apply to a wide range of orchid lineages.

Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses

Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the major challenges to users of these methods, such as selecting event costs and selecting representative reconciliations. Next, recent advances to address these challenges are discussed followed by a discussion of several established and recent software tools.

Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota

The degree of similarity between the microbiotas of host species often mirrors the phylogenetic proximity of the hosts. This pattern, referred to as phylosymbiosis, is widespread in animals and plants. While phylosymbiosis was initially interpreted as the signal of symbiotic transmission and coevolution between microbes and their hosts, it is now recognized that similar patterns can emerge even if the microbes are environmentally acquired. Distinguishing between these two scenarios, however, remains challenging. We recently developed HOME (host-microbiota evolution), a cophylogenetic model designed to detect vertically transmitted microbes and host switches from amplicon sequencing data. Here, we applied HOME to the microbiotas of Hawaiian spiders of the genus Ariamnes, which experienced a recent radiation on the archipelago. We demonstrate that although Hawaiian Ariamnes spiders display a significant phylosymbiosis, there is little evidence of microbial vertical transmission. Next, we performed simulations to validate the absence of transmitted microbes in Ariamnes spiders. We show that this is not due to a lack of detection power because of the low number of segregating sites or an effect of phylogenetically driven or geographically driven host switches. Ariamnes spiders and their associated microbes therefore provide an example of a pattern of phylosymbiosis likely emerging from processes other than vertical transmission.

IMPORTANCE How host-associated microbiotas assemble and evolve is one of the outstanding questions of microbial ecology. Studies aiming at answering this question have repeatedly found a pattern of “phylosymbiosis,” that is, a phylogenetic signal in the composition of host-associated microbiotas. While phylosymbiosis was often interpreted as evidence for vertical transmission and host-microbiota coevolution, simulations have now shown that it can emerge from other processes, including host filtering of environmentally acquired microbes. However, distinguishing the processes driving phylosymbiosis in nature remains challenging. We recently developed a cophylogenetic method that can detect vertical transmission. Here, we applied this method to the microbiotas of recently diverged spiders from the Hawaiian archipelago, which display a clear phylosymbiosis pattern. We found that none of the bacterial operational taxonomic units is vertically transmitted. We show with simulations that this result is not due to methodological artifacts. Thus, we provide a striking empirical example of phylosymbiosis emerging from processes other than vertical transmission.

Gene tree and species tree reconciliation with endosymbiotic gene transfer

MOTIVATION

It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree.

RESULTS

We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees.

AVAILABILITY AND IMPLEMENTATION

EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.

Do host habitat use and cospeciation matter in the evolution of Oswaldocruzia (Nematoda, Molineidae) from neotropical amphibians?

The genus Oswaldocruzia Travassos, 1917 includes approximately 90 species that are parasitic on amphibians and reptiles around the world, of which 43 occur in the neotropical region. However, molecular data supporting the taxonomic status of most species of the genus are scarce, and their phylogenetic relationships remain unknown. Using specimens of four molineid taxa (Oswaldocruzia belenensis Santos, Giese, Maldonado Jr. and Lanfredi, 2008; Oswaldocruzia chabaudi Ben Slimane & Durette-Desset, 1996, Oswaldocruzia chambrieri Ben Slimane & Durette-Desset, 1996 and Kentropyxia hylae Feitosa, Furtado, Santos and Melo, 2015) from amphibian hosts collected in different regions of Pará, Brazil, we conducted morphological studies, molecular analyses and phylogenies (maximum likelihood and Bayesian inference) using the cytochrome c oxidase subunity I (Cox1) gene. The newly generated sequences were compared with those of ten publicly available Cox1 sequences of Oswaldocruzia from Mexico. Our findings demonstrated significant differences between the sequences of amazonian specimens and sequences from specimens collected in Mexico, and we suggest that host-parasite cospeciation or habitat use might be related to molineid evolution in amphibian hosts. Additionally, this work presents new hosts and new geographical records for species of Oswaldocruzia from the neotropics.

Indirect identification of horizontal gene transfer

Several implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question “how much information about all HGT events is contained in LDT graphs” with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.

Diversity and characterization of bacterial communities of five co-occurring species at a hydrothermal vent on the Tonga Arc

Host-symbiont relationships in hydrothermal vent ecosystems, supported by chemoautotrophic bacteria as primary producers, have been extensively studied. However, the process by which densely populated co-occurring invertebrate hosts form symbiotic relationships with bacterial symbionts remains unclear. Here, we analyzed gill-associated symbiotic bacteria (gill symbionts) of five co-occurring hosts, three mollusks ("Bathymodiolus" manusensis, B. brevior, and Alviniconcha strummeri) and two crustaceans (Rimicaris variabilis and Austinograea alayseae), collected together at a single vent site in the Tonga Arc. We observed both different compositions of gill symbionts and the presence of unshared operational taxonomic units (OTUs). In addition, the total number of OTUs was greater for crustacean hosts than for mollusks. The phylogenetic relationship trees of gill symbionts suggest that γ-proteobacterial gill symbionts have coevolved with their hosts toward reinforcement of host specificity, while campylobacterial Sulfurovum species found across various hosts and habitats are opportunistic associates. Our results confirm that gill symbiont communities differ among co-occurring vent invertebrates and indicate that hosts are closely related with their gill symbiont communities. Considering the given resources available at a single site, differentiation of gill symbionts seems to be a useful strategy for obtaining nutrition and energy while avoiding competition among both hosts and gill symbionts.

A newly discovered radiation of endoparasitic gastropods and their coevolution with asteroid hosts in Antarctica

BACKGROUND

Marine invertebrates are abundant and diverse on the continental shelf in Antarctica, but little is known about their parasitic counterparts. Endoparasites are especially understudied because they often possess highly modified body plans that pose problems for their identification. Asterophila, a genus of endoparasitic gastropod in the family Eulimidae, forms cysts in the arms and central discs of asteroid sea stars. There are currently four known species in this genus, one of which has been described from the Antarctic Peninsula (A. perknasteri). This study employs molecular and morphological data to investigate the diversity of Asterophila in Antarctica and explore cophylogenetic patterns between host and parasite.

RESULTS

A maximum-likelihood phylogeny of Asterophila and subsequent species-delimitation analysis uncovered nine well-supported putative species, eight of which are new to science. Most Asterophila species were found on a single host species, but four species were found on multiple hosts from one or two closely related genera, showing phylogenetic conservatism of host use. Both distance-based and event-based cophylogenetic analyses uncovered a strong signal of coevolution in this system, but most associations were explained by non-cospeciation events.

DISCUSSION

The prevalence of duplication and host-switching events in Asterophila and its asteroid hosts suggests that synchronous evolution may be rare even in obligate endoparasitic systems. The apparent restricted distribution of Asterophila from around the Scotia Arc may be an artefact of concentrated sampling in the area and a low obvious prevalence of infection. Given the richness of parasites on a global scale, their role in promoting host diversification, and the threat of their loss through coextinction, future work should continue to investigate parasite diversity and coevolution in vulnerable ecosystems.

Tree shape-based approaches for the comparative study of cophylogeny

Cophylogeny is the congruence of phylogenetic relationships between two different groups of organisms due to their long-term interaction. We investigated the use of tree shape distance measures to quantify the degree of cophylogeny. We implemented a reverse-time simulation model of pathogen phylogenies within a fixed host tree, given cospeciation probability, host switching, and pathogen speciation rates. We used this model to evaluate 18 distance measures between host and pathogen trees including two kernel distances that we developed for labeled and unlabeled trees, which use branch lengths and accommodate different size trees. Finally, we used these measures to revisit published cophylogenetic studies, where authors described the observed associations as representing a high or low degree of cophylogeny. Our simulations demonstrated that some measures are more informative than others with respect to specific coevolution parameters especially when these did not assume extreme values. For real datasets, trees' associations projection revealed clustering of high concordance studies suggesting that investigators are describing it in a consistent way. Our results support the hypothesis that measures can be useful for quantifying cophylogeny. This motivates their usage in the field of coevolution and supports the development of simulation-based methods, i.e., approximate Bayesian computation, to estimate the underlying coevolutionary parameters.

The joint evolution of the Myxozoa and their alternate hosts: A cnidarian recipe for success and vast biodiversity

The relationships between parasites and their hosts are intimate, dynamic and complex; the evolution of one is inevitably linked to the other. Despite multiple origins of parasitism in the Cnidaria, only parasites belonging to the Myxozoa are characterized by a complex life cycle, alternating between fish and invertebrate hosts, as well as by high species diversity. This inspired us to examine the history of adaptive radiations in myxozoans and their hosts by determining the degree of congruence between their phylogenies and by timing the emergence of myxozoan lineages in relation to their hosts. Recent genomic analyses suggested a common origin of Polypodium hydriforme, a cnidarian parasite of acipenseriform fishes, and the Myxozoa, and proposed fish as original hosts for both sister lineages. We demonstrate that the Myxozoa emerged long before fish populated Earth and that phylogenetic congruence with their invertebrate hosts is evident down to the most basal branches of the tree, indicating bryozoans and annelids as original hosts and challenging previous evolutionary hypotheses. We provide evidence that, following invertebrate invasion, fish hosts were acquired multiple times, leading to parallel cospeciation patterns in all major phylogenetic lineages. We identify the acquisition of vertebrate hosts that facilitate alternative transmission and dispersion strategies as reason for the distinct success of the Myxozoa, and identify massive host specification-linked parasite diversification events. The results of this study transform our understanding of the origins and evolution of parasitism in the most basal metazoan parasites known.

Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss Model

Phylogenetic tree reconciliation is widely used in the fields of molecular evolution, cophylogenetics, parasitology, and biogeography to study the evolutionary histories of pairs of entities. In these contexts, reconciliation is often performed using maximum parsimony under the Duplication-Transfer-Loss (DTL) event model. In general, the number of maximum parsimony reconciliations (MPRs) can grow exponentially with the size of the trees. While a number of previous efforts have been made to count the number of MPRs, find representative MPRs, and compute the frequencies of events across the space of MPRs, little is known about the structure of MPR space. In particular, how different are MPRs in terms of the events that they comprise? One way to address this question is to compute the diameter of MPR space, defined to be the maximum number of DTL events that distinguish any two MPRs in the solution space. We show how to compute the diameter of MPR space in polynomial time and then apply this algorithm to a large biological dataset to study the variability of events.

A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains

Recent horizontal gene transfer (HGT) is crucial for enabling microbes to rapidly adapt to their novel environments without relying upon rare beneficial mutations that arise spontaneously. For several years now, computational approaches have been developed to detect HGT, but they typically lack the sensitivity and ability to detect recent HGT events. Here we introduce a novel strategy, named RecentHGT. The number of genes undergoing recent HGT between two bacterial genomes was estimated by a new algorithm derived from the expectation-maximization algorithm and is based on the theoretical sequence-similarity distribution of orthologous genes. We tested the proposed strategy by applying it to a set of 10 Rhizobium genomes, and detected several large-scale recent HGT events. We also found that our strategy was more sensitive than other available HGT detection methods. These HGT events were mainly mediated by symbiotic plasmids. Our new strategy can provide clear evidence of recent HGT events and thus it brings us closer to the goal of detecting these potentially adaptive evolution processes in rhizobia as well as pathogens.

DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations

Phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of species and genes and other dependent entities. Reconciliation is typically performed in a maximum parsimony framework and the number of optimal reconciliations can grow exponentially with the size of the trees, making it difficult to understand the solution space. This paper demonstrates how a small number of reconciliations can be found that collectively contain the most highly supported events in the solution space. While we show that the formal problem is NP-complete, we give a approximation algorithm, experimental results that indicate its effectiveness, and the new DTL-RnB software tool that uses our algorithms to summarize the space of optimal reconciliations (www.cs.hmc.edu/dtlrnb).

Tanglegrams: A Reduction Tool for Mathematical Phylogenetics

Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of study in coevolutionary analysis. Although there has been considerable work on planar drawings of tanglegrams, they have not been fully explored as combinatorial objects until recently. In this paper, we describe how many discrete mathematical questions on trees "factor" through a problem on tanglegrams, and how understanding that factoring can simplify analysis. Depending on the problem, it may be useful to consider a unordered version of tanglegrams, and/or their unrooted counterparts. For all of these definitions, we show how the isomorphism types of tanglegrams can be understood in terms of double cosets of the symmetric group, and we investigate their automorphisms. Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.

Environmental heterogeneity and the evolution of plant-virus interactions: Viruses in wild pepper populations

Understanding host-pathogen interactions requires analyses to address the multiplicity of scales in heterogeneous landscapes. Anthropogenic influence on plant communities, especially cultivation, is a major cause of environmental heterogeneity. We have approached the analysis of how environmental heterogeneity determines plant-virus interactions by studying virus infection in a wild plant currently undergoing incipient domestication, the wild pepper or chiltepin, across its geographical range in Mexico. We have shown previously that anthropogenic disturbance is associated with higher infection and disease risk, and with disrupted patterns of host and virus genetic spatial structure. We now show that anthropogenic factors, species richness, host genetic diversity and density in communities supporting chiltepin differentially affect infection risk according to the virus analysed. We also show that in addition to these factors, a broad range of abiotic and biotic variables meaningful to continental scales, have an important role on the risk of infection depending on the virus. Last, we show that natural virus infection of chiltepin plants in wild communities results in decreased survival and fecundity, hence negatively affecting fitness. This important finding paves the way for future studies on plant-virus co-evolution.

DTL reconciliation repair

Background

Maximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs. Since the problem of finding temporally feasible maximum parsimony reconciliations is NP-complete, current methods use either exact algorithms with exponential worst-case running time or heuristics that do not guarantee optimal solutions.

Results

We offer an efficient new approach that begins with a potentially infeasible maximum parsimony reconciliation and iteratively “repairs” it until it becomes temporally feasible.

Conclusions

In a non-trivial number of cases, this approach finds solutions that are better than those found by the widely-used Jane heuristic.

Testing cospeciation through large-scale cophylogenetic studies

Insects are involved in a multitude of interactions with other organisms, which make them ideal models for large-scale cophylogenetic studies. Once phylogenies of interacting lineages have been inferred, there are a number of questions we may wish to ask, such as what was the relationship between the partners in the past? Have they co-evolved for thousands or millions of years, or has one of the partners switched among different host species? To answer such questions, researchers may conduct cophylogenetic analysis, to explore the relationships between the phylogenies of interacting lineages and determine whether the match is significant or find explanations for observed differences. When combined with dating analyses, cophylogenetic analyses may support cospeciation of the partners or phylogenetic tracking. As they may reveal dynamics of host-pathogen coevolution, cophylogenetic studies may also help tackle global health issues (e.g. document the spread of disease causing pathogens). Cophylogenetic studies of parasitoids and their insect hosts may also help identify effective biocontrol agents. With the advent of next generation sequencing technologies and keeping in mind that systematic errors may occur, cophylogenetics will benefit from better-resolved trees, allowing more accurate reconciliation. However as trees become larger, current algorithms also become more computationally challenging. Nevertheless, both theoretical and methodological developments are leading to more accurate and powerful tests of cospeciation through cophylogenetic analysis.

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees

Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host-parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a "compass" when "walking" through jungles of tangled phylogenetic trees.

An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism

An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats.

The Importance of Fossils in Understanding the Evolution of Parasites and Their Vectors

Knowledge concerning the diversity of parasitism and its reach across our current understanding of the tree of life has benefitted considerably from novel molecular phylogenetic methods. However, the timing of events and the resolution of the nature of the intimate relationships between parasites and their hosts in deep time remain problematic. Despite its vagaries, the fossil record provides the only direct evidence of parasites and parasitism in the fossil record of extant and extinct lineages. Here, we demonstrate the potential of the fossil record and other lines of geological evidence to calibrate the origin and evolution of parasitism by combining different kinds of dating evidence with novel molecular clock methodologies. Other novel methods promise to provide additional evidence for the presence or the life habit of pathogens and their vectors, including the discovery and analysis of ancient DNA and other biomolecules, as well as computed tomographic methods.

Do the historical biogeography and evolutionary history of the digenean Margotrema spp. across central Mexico mirror those of their freshwater fish hosts (Goodeinae)?

Host-parasite systems provide an ideal platform to study evolution at different levels, including codivergence in a historical biogeography context. In this study we aim to describe biogeographic and codivergent patterns and associated processes of the Goodeinae freshwater fish and their digenean parasite (Margotrema spp.) over the last 6.5 Ma (million years), identifying the main factors (host and/or hydrogeomorphology) that influenced the evolution of Margotrema. We obtained a species tree for Margotrema spp. using DNA sequence data from mitochondrial and nuclear molecular markers (COI and ITS1, respectively) and performed molecular dating to discern divergence events within the genus. The dispersal-extinction-cladogenesis (DEC) model was used to describe the historical biogeography of digeneans and applied to cophylogenetic analyses of Margotrema and their goodeine hosts. Our results showed that the evolutionary history of Margotrema has been shaped in close association with its geographic context, especially with the geological history of central Mexico during the Pleistocene. Host-specificity has been established at three levels of historical association: a) Species-Species, represented by Xenotaenia resolanae-M. resolanae exclusively found in the Cuzalapa River Basin; b) Species-Lineage, represented by Characodon audax-M. bravoae Lineage II, exclusive to the Upper and Middle Mezquital River Basin, and c) Tribe-Lineage, including two instances of historical associations among parasites and hosts at the taxonomical level of tribe, one represented by Ilyodontini-M. bravoae Lineage I (distributed across the Ayuquila and Balsas River Basins), and another comprised of Girardinichthyini/Chapalichthyini-M. bravoae Lineage III, found only in the Lerma River Basin. We show that the evolutionary history of the parasites is, on several occasions, in agreement with the phylogenetic and biogeographic history of their hosts. A series of biogeographic and host-parasite events explain the codivergence patterns observed, in which cospeciation and colonisation via host-switching and vicariant plus dispersal events are appreciated, at different times during the diversification history of both associates, particularly during the Pleistocene.

Reconciliation of gene and species trees

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.

Changes in diversification patterns and signatures of selection during the evolution of murinae-associated hantaviruses

In the last 50 years, hantaviruses have significantly affected public health worldwide, but the exact extent of the distribution of hantavirus diseases, species and lineages and the risk of their emergence into new geographic areas are still poorly known. In particular, the determinants of molecular evolution of hantaviruses circulating in different geographical areas or different host species are poorly documented. Yet, this understanding is essential for the establishment of more accurate scenarios of hantavirus emergence under different climatic and environmental constraints. In this study, we focused on Murinae-associated hantaviruses (mainly Seoul Dobrava and Hantaan virus) using sequences available in GenBank and conducted several complementary phylogenetic inferences. We sought for signatures of selection and changes in patterns and rates of diversification in order to characterize hantaviruses’ molecular evolution at different geographical scales (global and local). We then investigated whether these events were localized in particular geographic areas. Our phylogenetic analyses supported the assumption that RNA virus molecular variations were under strong evolutionary constraints and revealed changes in patterns of diversification during the evolutionary history of hantaviruses. These analyses provide new knowledge on the molecular evolution of hantaviruses at different scales of time and space.

An extreme case of plant-insect codiversification: 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 cophylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on an average, wasps had sequences from 77% of 6 genes (5.6 kb), figs had sequences from 60% of 5 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 cophylogenetic analyses further support the codiversification hypothesis. Biogeographic analyses indicate that the present-day distribution of fig and pollinator lineages is consistent with a 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 codiversification. [Biogeography; coevolution; cospeciation; host switching; long-branch attraction; phylogeny.].

Evolutionary history of nematodes associated with sweat bees

Organisms that live in close association with other organisms make up a large part of the world's diversity. One driver of this diversity is the evolution of host-species specificity, which can occur via reproductive isolation following a host-switch or, given the correct circumstances, via cospeciation. In this study, we explored the diversity and evolutionary history of Acrostichus nematodes that are associated with halictid bees in North America. First, we conducted surveys of bees in Virginia, and found six halictid species that host Acrostichus. To test the hypothesis of cospeciation, we constructed phylogenetic hypotheses of Acrostichus based on three genes. We found Acrostichus puri and Acrostichus halicti to be species complexes comprising cryptic, host-specific species. Although several nodes in the host and symbiont phylogenies were congruent and tests for cospeciation were significant, the host's biogeography, the apparent patchiness of the association across the host's phylogeny, and the amount of evolution in the nematode sequence suggested a mixture of cospeciation, host switching, and extinction events instead of strict cospeciation. Cospeciation can explain the relationships between Ac. puri and its augochlorine hosts, but colonization of Halictus hosts is more likely than cospeciation. The nematodes are vertically transmitted, but sexual transmission is also likely. Both of these transmission modes may explain host-species specificity and congruent bee and nematode phylogenies. Additionally, all halictid hosts come from eusocial or socially polymorphic lineages, suggesting that sociality may be a factor in the suitability of hosts for Acrostichus.

Some like it hot: evolution and ecology of novel endosymbionts in bat flies of cave-roosting bats (hippoboscoidea, nycterophiliinae)

We investigated previously unknown associations between bacterial endosymbionts and bat flies of the subfamily Nycterophiliinae (Diptera, Streblidae). Molecular analyses revealed a novel clade of Gammaproteobacteria in Nycterophilia bat flies. This clade was not closely related to Arsenophonus-like microbes found in its sister genus Phalconomus and other bat flies. High population infection rates in Nycterophilia across a wide geographic area, the presence of the symbionts in pupae, the general codivergence between hosts and symbionts, and high AT composition bias in symbiont genes together suggest that this host-symbiont association is obligate in nature and ancient in origin. Some Nycterophilia samples (14.8%) also contained Wolbachia supergroup F (Alphaproteobacteria), suggesting a facultative symbiosis. Likelihood-based ancestral character mapping revealed that, initially, obligate symbionts exhibited association with host-specific Nycterophilia bat flies that use a broad temperature range of cave environments for pupal development. As this mutualism evolved, the temperature range of bat flies narrowed to an exclusive use of hot caves, which was followed by a secondary broadening of the bat flies' host associations. These results suggest that the symbiosis has influenced the environmental tolerance of parasite life history stages. Furthermore, the contingent change to an expanded host range of Nycterophilia bat flies upon narrowing the ecological niche of their developmental stages suggests that altered environmental tolerance across life history stages may be a crucial factor in shaping parasite-host relationships.

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.

RESULTS

We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000-fold speed-up over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous evolutionary analyses of large gene families and enables its use in advanced reconciliation-based gene and species tree reconstruction methods.

AVAILABILITY

Our programs can be freely downloaded from http://compbio.mit.edu/ranger-dtl/.

Complex patterns of host switching in New World arenaviruses

We empirically tested the long-standing hypothesis of codivergence of New World arenaviruses (NWA) with their hosts. We constructed phylogenies for NWA and all known hosts and used them in reconciliation analyses. We also constructed a phylogenetic tree of all Sigmodontinae and Neotominae rodents and tested whether viral-host associations were phylogenetically clustered. We determined host geographical overlap to determine to what extent opportunity to switch hosts was limited by host relatedness or physical proximity. With the exception of viruses from North America, no phylogenetically codivergent pattern between NWA and their hosts was found. We found that different virus clades were clustered differently and that Clade B with members pathogenic to humans was randomly distributed across the rodent phylogeny. Furthermore, viral relatedness within Clade B was significantly explained by the geographic overlap of their hosts' ranges rather than host relatedness, indicating that they are capable of host switching opportunistically. This has important bearings on their potential to become panzootic. Together, these analyses suggest that NWA have not codiverged with their hosts and instead have evolved predominantly via host switching.

Shared ancestry between a newfound mole-borne hantavirus and hantaviruses harbored by cricetid rodents

Discovery of genetically distinct hantaviruses in multiple species of shrews (order Soricomorpha, family Soricidae) and moles (family Talpidae) contests the conventional view that rodents (order Rodentia, families Muridae and Cricetidae) are the principal reservoir hosts and suggests that the evolutionary history of hantaviruses is far more complex than previously hypothesized. We now report on Rockport virus (RKPV), a hantavirus identified in archival tissues of the eastern mole (Scalopus aquaticus) collected in Rockport, TX, in 1986. Pairwise comparison of the full-length S, M, and L genomic segments indicated moderately low sequence similarity between RKPV and other soricomorph-borne hantaviruses. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that RKPV shared a most recent common ancestor with cricetid-rodent-borne hantaviruses. Distributed widely across the eastern United States, the fossorial eastern mole is sympatric and syntopic with cricetid rodents known to harbor hantaviruses, raising the possibility of host-switching events in the distant past. Our findings warrant more-detailed investigations on the dynamics of spillover and cross-species transmission of present-day hantaviruses within communities of rodents and moles.

A parameter-adaptive dynamic programming approach for inferring cophylogenies

Background

Coevolutionary systems like hosts and their parasites are commonly used model systems for evolutionary studies. Inferring the coevolutionary history based on given phylogenies of both groups is often done by employing a set of possible types of events that happened during coevolution. Costs are assigned to the different types of events and a reconstruction of the common history with a minimal sum of event costs is sought.

Results

This paper introduces a new algorithm and a corresponding tool called CoRe-PA, that can be used to infer the common history of coevolutionary systems. The proposed method utilizes an event-based concept for reconciliation analyses where the possible events are cospeciations, sortings, duplications, and (host) switches. All known event-based approaches so far assign costs to each type of cophylogenetic events in order to find a cost-minimal reconstruction. CoRe-PA uses a new parameter-adaptive approach, i.e., no costs have to be assigned to the coevolutionary events in advance. Several biological coevolutionary systems that have already been studied intensely in literature are used to show the performance of CoRe-PA.

Conclusion

From a biological point of view reasonable cost values for event-based reconciliations can often be estimated only very roughly. CoRe-PA is very useful when it is difficult or impossible to assign exact cost values to different types of coevolutionary events in advance.

Evolutionary insights from a genetically divergent hantavirus harbored by the European common mole (Talpa europaea)

BACKGROUND

The discovery of genetically distinct hantaviruses in shrews (Order Soricomorpha, Family Soricidae) from widely separated geographic regions challenges the hypothesis that rodents (Order Rodentia, Family Muridae and Cricetidae) are the primordial reservoir hosts of hantaviruses and also predicts that other soricomorphs harbor hantaviruses. Recently, novel hantavirus genomes have been detected in moles of the Family Talpidae, including the Japanese shrew mole (Urotrichus talpoides) and American shrew mole (Neurotrichus gibbsii). We present new insights into the evolutionary history of hantaviruses gained from a highly divergent hantavirus, designated Nova virus (NVAV), identified in the European common mole (Talpa europaea) captured in Hungary.

METHODOLOGY/PRINCIPAL FINDINGS

Pair-wise alignment and comparison of the full-length S- and L-genomic segments indicated moderately low sequence similarity of 54-65% and 46-63% at the nucleotide and amino acid levels, respectively, between NVAV and representative rodent- and soricid-borne hantaviruses. Despite the high degree of sequence divergence, the predicted secondary structure of the NVAV nucleocapsid protein exhibited the characteristic coiled-coil domains at the amino-terminal end, and the L-segment motifs, typically found in hantaviruses, were well conserved. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that NVAV formed a distinct clade that was evolutionarily distant from all other hantaviruses.

CONCLUSIONS

Newly identified hantaviruses harbored by shrews and moles support long-standing virus-host relationships and suggest that ancestral soricomorphs, rather than rodents, may have been the early or original mammalian hosts.

Assessment of codivergence of mastreviruses with their plant hosts

BACKGROUND

Viruses that have spent most of their evolutionary time associated with a single host lineage should have sequences that reflect codivergence of virus and host. Several examples for RNA viruses of host-virus tree congruence are being challenged. DNA viruses, such as mastreviruses, are more likely than RNA viruses to have maintained a record of host lineage association.

RESULTS

The full genomes of 28 isolates of Wheat dwarf virus (WDV), a member of the Mastrevirus genus, from different regions of China were sequenced. The analysis of these 28 entire genomes and 18 entire genome sequences of cereal mastreviruses from other countries support the designation of wheat, barley and oat mastrevirus isolates as separate species. They revealed that relative divergence times for the viruses WDV, Barley dwarf virus (BDV), Oat dwarf virus (ODV) and Maize streak virus (MSV) are proportional to divergence times of their hosts, suggesting codivergence. Considerable diversity among Chinese isolates was found and was concentrated in hot spots in the Rep A, SIR, LIR, and intron regions in WDV genomes. Two probable recombination events were detected in Chinese WDV isolates. Analysis including further Mastrevirus genomes concentrated on coding regions to avoid difficulties due to recombination and hyperdiversity. The analysis demonstrated congruence of trees in two branches of the genus, but not in the third. Assuming codivergence, an evolutionary rate of 10-8 substitutions per site per year was calculated. The low rate implies stronger constraints against change than are obtained by other methods of estimating the rate.

CONCLUSION

We report tests of the hypothesis that mastreviruses have codiverged with their monocotyledonous hosts over 50 million years of evolution. The tests support the hypothesis for WDV, BDV and ODV, but not for MSV and other African streak viruses.

Host-bacterial coevolution and the search for new drug targets

Understanding the coevolution between humans and our microbial symbionts and pathogens requires complementary approaches, ranging from community analysis to in-depth analysis of individual genomes. Here we review the evidence for coevolution between symbionts and their hosts, the role of horizontal gene transfer in coevolution, and genomic and metagenomic approaches to identify drug targets. Recent studies have shown that our symbiotic microbes confer many metabolic capabilities that our mammalian genomes lack, and that targeting mechanisms of horizontal gene transfer is a promising new direction for drug discovery. Gnotobiotic ('germ-free') mice are an especially exciting new tool for unraveling the function of microbes, whether individually or in the context of complex communities.

Parasites: proxies for host genealogy and ecology?

Genetic information is used extensively to reconstruct the evolutionary and demographic history of organisms. Recently, it has been suggested that genetic information from some parasites can complement genetic data from their hosts. This approach relies upon the hypothesis that such parasites share a common history with their host. In some cases, parasites provide an additional source of information because parasite data can better reconstruct the common history. Here, we discuss which parasite traits are important in determining their usefulness for analysing host history. The key is the matching of the traits of the parasite (e.g. effective population size, generation time, mutation rate and level of host specificity) with the timescales (phylogenetic, phylogeographic and demographic) that are relevant to the issues of concern in host history.