Multiple cophylogenetic analyses reveal frequent cospeciation between pelecaniform birds and Pectinopygus lice

Lice in the genus Pectinopygus parasitize a single order of birds (Pelecaniformes). To examine the degree of congruence between the phylogenies of 17 Pectinopygus species and their pelecaniform hosts, sequences from mitochondrial 12S rRNA, 16S rRNA, COI, and nuclear wingless and EF1-alpha genes (2290 nucleotides) and from mitochondrial 12S rRNA, COI, and ATPases 8 and 6 genes (1755 nucleotides) were obtained for the lice and the birds, respectively. Louse data partitions were analyzed for evidence of incongruence and evidence of long-branch attraction prior to cophylogenetic analyses. Host-parasite coevolution was studied by different methods: TreeFitter, TreeMap, ParaFit, likelihood-ratio test, data-based parsimony method, and correlation of coalescence times. All methods agree that there has been extensive cospeciation in this host-parasite system, but the results are sensitive to the selection of different phylogenetic hypotheses and analytical methods for evaluating cospeciation. Perfect congruence between phylogenies is not found in this association, probably as a result of occasional host switching by the lice. Errors due to phylogenetic reconstruction methods, incorrect or incomplete taxon sampling, or to different loci undergoing different evolutionary histories cannot be rejected, thus emphasizing the need for improved cophylogenetic methodologies.     

Host shift and cospeciation rate estimation from co‐phylogenies

Host shifts can cause novel infectious diseases, and is a key process in diversification. Disentangling the effects of host shift vs. those of cospeciation is non‐trivial as both can result in phylogenic congruence. We develop a new framework based on network analysis and Approximate Bayesian Computation to quantify host shift and cospeciation rates in host‐parasite systems. Our method enables estimation of the expected time to the next host shift or cospeciation event. We then apply it to avian haemosporidian parasite systems and to the pocket gophers‐chewing lice system, and demonstrate that both host shift and cospeciation can be reliably estimated by our method. We confirm that host shifts have shaped the evolutionary history of avian haemosporidian parasites and have played a minor role in the gopher–chewing lice system. Our method is promising for predicting the rate of potential host shifts and thus the emergence of novel infectious diseases.     

Unravelling evolutionary relationships between epifoliar Meliolaceae and angiosperms

Epifoliar fungi are a group of poorly studied fungal symbionts that coinhabit the surface of living plants. Meliolaceae is the largest group of epifoliar fungi and has been considered as obligate parasites. We investigated the taxonomy of Meliolaceae and the coevolutionary events with their host plants using time-calibrated cophylogeny based on large subunit, small subunit, and internal transcribed spacer (ITS) sequence data obtained from 17 different fungal taxa and rbcL, ITS, and trnH-psbA sequence data from their corresponding hosts. Nine new fungal species are introduced in this paper and Appendiculella is synonymized under Asteridiella. The dominant coevolutionary events during the Cretaceous and Cenozoic are cospeciation and host shift, respectively. We hypothesize that the evolutionary history of epifoliar fungi can be divided into three major periods: origins of families, formations of genera, and diversification of species. The rise of angiosperms prompted the evolution of modern epifoliar fungi and the diversification of orders of Angiospermae fostered the formation of epifoliar fungal genera. Phylogenetically, epifoliar fungal genera can be delimited according to their coevolutionary patterns and divergent periods.     

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.     

Coevolution between Lamellodiscus (Monogenea: Diplectanidae) and Sparidae (Teleostei): the study of a complex host-parasite system

Abstract.— Host-parasite coevolution was studied between Sparidae (Teleostei) fishes and their parasites of the genus Lamellodiscus (Monogenea, Diplectanidae) in the northwestern Mediterranean Sea. Molecular phylogenies were reconstructed for both groups. The phylogenetic tree of the Sparidae was obtained from previously published 16S mitochondrial DNA (mtDNA) sequences associated with new cytochrome-b mtDNA sequences via a "total evidence" procedure. The phylogeny of Lamellodiscus species was reconstructed from 18S rDNA sequences that we obtained. Host-parasite coevolution was studied through different methods: TreeFitter, TreeMap, and a new method, ParaFit. If the cost of a host switch is not assumed to be high for parasites, all methods agree on the absence of widespread cospeciation processes in this host-parasite system. Host-parasite associations were interpreted to be due more to ecological factors than to coevolutionary processes. Host specificity appeared not to be related to host-parasite cospeciation.     

Host switch leads to emergence of Plasmodium vivax malaria in humans

The geographical origin of Plasmodium vivax, the most widespread human malaria parasite, is controversial. Although genetic closeness to Asian primate malarias has been confirmed by phylogenetic analyses, genetic similarities between P. vivax and Plasmodium simium, a New World primate malaria, suggest that humans may have acquired P. vivax from New World monkeys or vice versa. Additionally, the near fixation of the Duffy-negative blood type (FY x B(null)/FY x B(null)) in West and Central Africa, consistent with directional selection, and the association of Duffy negativity with complete resistance to vivax malaria suggest a prolonged period of host-parasite coevolution in Africa. Here we use Bayesian and likelihood methods in conjunction with cophylogeny mapping to reconstruct the genetic and coevolutionary history of P. vivax from the complete mitochondrial genome of 176 isolates as well as several closely related Plasmodium species. Taken together, a haplotype network, parasite migration patterns, demographic history, and cophylogeny mapping support an Asian origin via a host switch from macaque monkeys.     

RECONSTRUCTING THE HISTORY OF HOST-PARASITE ASSOCIATIONS USING GENERALISED PARSIMONY

Abstract — In reconstructing the history of host-parasite associations, it is necessary to consider several different processes, such as cospeciation and host switching, that may affect an association. A simple reconstruction method is to maximise the number of host-parasite cospeciations. However, maximum cospeciation reconstruction may require the postulation of a large number of other kinds of events, such as parasite extinction or exclusion from certain hosts. A more sophisticated method associates each kind of event with a cost or weight which is inversely related to the likelihood of that kind of event occurring. I present a method of the latter type that distinguishes between two different processes: host tracking, of which cospeciation is a special case, and host switching. Given a relative weight for these two types of events, it is possible to convert the host phytogeny into a cost matrix, allowing for host switching, and use generalised-parsimony algorithms to find minimum-cost reconstructions of the history of the host-parasite association. Different relative switch weights give different minimum-cost reconstructions; the optimal switch weight can be found by maximising the fit between the tracking events and the parasite phytogeny, controlling for the number of postulated switches. As an empirical application of the method, data on an association between pocket gophers and their parasitic chewing lice were re-examined. Although these data have been extensively analysed previously, the generalised parsimony approach throws new light on the history of the association.     

Inferring processes of coevolutionary diversification in a community of Panamanian strangler figs and associated pollinating wasps*

The fig and pollinator wasp obligate mutualism is diverse (～750 described species), ecologically important, and ancient (～80 Ma). Once thought to be an example of strict one‐to‐one cospeciation, current thinking suggests genera of pollinator wasps codiversify with corresponding sections of figs, but the degree to which cospeciation or other processes contribute to the association at finer scales is unclear. Here, we use genome‐wide sequence data from a community of Panamanian strangler figs and associated wasp pollinators to estimate the relative contributions of four evolutionary processes generating cophylogenetic patterns in this mutualism: cospeciation, host switching, pollinator speciation, and pollinator extinction. Using a model‐based approach adapted from the study of gene family evolution, our results demonstrate the importance of host switching of pollinator wasps at this fine phylogenetic and regional scale. Although we estimate a modest amount of cospeciation, simulations reveal the number of putative cospeciation events to be consistent with what would be expected by chance. Additionally, model selection tests identify host switching as a critical parameter for explaining cophylogenetic patterns in this system. Our study demonstrates a promising approach through which the history of evolutionary association between interacting lineages can be rigorously modeled and tested in a probabilistic phylogenetic framework.     

A cophylogenetic perspective of RNA-virus evolution

The extent to which viruses and their hosts codiverge remains an open question, given that numerous cases of both "cospeciation" and horizontal switching have recently been documented. DNA viruses that form persistent infections are thought to be the most likely candidates for phylogenetic congruence. Phylogenetic reconciliation analysis was used to compare established phylogenies for four RNA viruses and their hosts. The analysis employs a cophylogeny mapping technique, implemented in TreeMap v2.0, to find the most parsimonious combinations of evolutionary events able to reconcile any incongruence. This technique is guaranteed to recover all potentially optimal solutions to the reconciled tree and specifically tests the null hypothesis that an associate phylogeny is no more congruent with a host phylogeny than would be a random tree with the same taxon set. Phylogenies for Hantavirus, Spumavirus, and avian sarcoma leukosis virus were found to be significantly similar to their host trees, whereas Lyssavirus and Arenavirus displayed no significant congruence. These results demonstrate that RNA viruses are able to form stable associations with their hosts over evolutionary time scales and that the details of such associations are consistent with persistent infection being a necessary but not sufficient precondition.     

Monogeneans of West African cichlid fish: evolution and cophylogenetic interactions

The goals of this paper were to investigate phylogenetic and evolutionary patterns of cichlid fish from West Africa and their Cichlidogyrus and Scutogyrus monogenean parasites, to uncover the presence of host-parasite cospeciation and to assess the level of morphological adaptation in parasites. This required the following steps, each one representing specific objectives of this paper: (1) to build phylogenetic trees for Cichlidogyrus and Scutogyrus species based on ribosomal DNA sequences, (2) to investigate phylogenetic relationships within West African cichlid fish based on the analysis of mitochondrial cytochrome b DNA sequences, (3) to investigate host-parasite cophylogenetic history to gain clues on parasite speciation process, and (4) to investigate the link between the morphology of the attachment apparatus and parasite phylogeny. Phylogenetic analyses supported the monophyletic origin of the Cichlidogyrus/Scutogyrus group, and suggested that Cichlidogyrus is polyphyletic and that Scutogyrus is monophyletic. The phylogeny of Cichlidae supported the separation of mouthbrooders and substrate-brooders and is consistent with the hypothesis that the mouthbrooding behavior of Oreochromis and Sarotherodon evolved from substrate-brooding behavior. The mapping of morphological characters of the haptor onto the parasite phylogenetic tree suggests that the attachment organ has evolved from a very simple form to a more complex one. The cophylogenetic analyses indicated a significant fit between trees using distance-based tests, but no significant cospeciation signal using tree-based tests, suggesting the presence of parasite duplications and host switches on related host species. This shed some light on the diversification process of Cichlidogyrus species parasitizing West African cichlids.     

Three-Dimensional Cost-Matrix Optimization and Maximum Cospeciation

In recent years, event-based approaches have been gaining ground in coevolutionary and biogeographical inference. Unlike pattern-based methods, event-based protocols deal directly with evolutionary events, such as dispersals and host switches. Three protocols have been proposed to date: (1) a coevolutionary method based on optimization of a standard two-dimensional cost matrix; (2) dispersal–vicariance analysis, based on optimization of a three-dimensional cost matrix; and (3) the maximum cospeciation method, thus far not considered a cost matrix method. I describe here general three-dimensional cost matrix optimization algorithms and how they can be applied to the maximum cospeciation problem. The new algorithms demonstrate that all existing event-based protocols, as well as possible future methods based on more complicated process models, can be incorporated into the three-dimensional cost matrix optimization framework.     

基因流存在条件下的物种形成研究述评:生殖隔离机制进化

物种形成过程是生物多样性形成的基础, 长期以来一直是进化生物学的中心议题之一。传统的异域物种形成理论认为, 地理隔离是物种分化的主要决定因子, 物种形成只有在种群之间存在地理隔离的情况下才能发生。近年来, 随着种群基因组学的发展和溯祖理论分析方法的完善, 种群间存在基因流情况下的物种形成成为进化生物学领域新的研究焦点。物种形成过程中是否有基因流的发生?基因流如何影响物种的形成与分化?基因流存在条件下物种形成的生殖隔离机制是什么?根据已发表的相关文献资料, 作者综述了当前物种形成研究中基因流的时间和空间分布模式、基因流对物种分化的影响以及生殖隔离机制形成等问题, 指出基因流存在条件下的物种形成可能是自然界普遍发生的一种模式。     

PARALLEL PHYLOGENIES: RECONSTRUCTING THE HISTORY OF HOST-PARASITE ASSEMBLAGES

Abstract— A method for reconstructing the history of a host-parasite assemblage is described. This method has the advantage of making explicit the relationship between the host and parasite trees, and it allows a visually intuitive representation of that history. It also enables host switches to be incorporated as an explanation of the observed pattern of host-parasite associations, without the spurious overestimates of the number of host switches that can be obtained using Brooks parsimony analysis (BPA). Reconstructions that maximize the number of cospeciation events have the greatest explanatory power and are hence preferred over reconstructions with fewer cospeciation events. A heuristic algorithm to find a single maximal reconstruction, and an exact algorithm to find all such reconstructions are presented. Two empirical applications of the method are given.     

Pseudocospeciation of the mycoparasite Cosmospora with their fungal hosts

Species of Cosmospora are parasites of other fungi (mycoparasites), including species belonging to the Xylariales. Based on prior taxonomic work, these fungi were determined to be highly host specific. We suspected that the association of Cosmospora and their hosts could not be a result of random chance, and tested the cospeciation of Cosmospora and the their hosts with contemporary methods (e.g., ParaFit, PACo, and Jane). The cophylogeny of Cosmospora and their hosts was found to be congruent, but only host‐parasite links in more recent evolutionary lineages of the host were determined as coevolutionary. Reconciliation reconstructions determined at least five host‐switch events early in the evolution of Cosmospora. Additionally, the rates of evolution between Cosmospora and their hosts were unequal. This pattern is more likely to be explained by pseudocospeciation (i.e., host switches followed by cospeciation), which also produces congruent cophylogenies.     

The cophylogeny of populations and cultures: reconstructing the evolution of Iranian tribal craft traditions using trees and jungles

Phylogenetic approaches to culture have shed new light on the role played by population dispersals in the spread and diversification of cultural traditions. However, the fact that cultural inheritance is based on separate mechanisms from genetic inheritance means that socially transmitted traditions have the potential to diverge from population histories. Here, we suggest that associations between these two systems can be reconstructed using techniques developed to study cospeciation between hosts and parasites and related problems in biology. Relationships among the latter are patterned by four main processes: co-divergence, intra-host speciation (duplication), intra-host extinction (sorting) and horizontal transfers. We show that patterns of cultural inheritance are structured by analogous processes, and then demonstrate the applicability of the host-parasite model to culture using empirical data on Iranian tribal populations.     

STATISTICAL TESTS OF HOST-PARASITE COSPECIATION

A history of cospeciation (synchronous speciation) among ecologically associated, but otherwise distantly related, species is often revealed by a strong correspondence of their phylogenies. In this paper, we present several tests of cospeciation that use maximum-likelihood and Bayesian methods of phylogenetic estimation. The hypotheses tested include: (1) topological agreement of phylogenies for coevolving groups; (2) identical speciation times of associated species; and (3) identical evolutionary rates in genes of associated species. These tests are applied to examine a possible instance of host-parasite coevolution among pocket gophers and lice using mitochondrial COI DNA sequences. The observed differences between gopher and louse trees cannot be explained by sampling error and are consistent with a rate of host switching about one-third the host speciation rate. A subset of the gopher-louse data is consistent with a common history of evolution (i.e., the topologies and speciation times are identical). However, the relative rate of nucleotide substitution is two to four times higher in the lice than in the gophers.     

Evolutionary relationships, cospeciation, and host switching in avian malaria parasites

We used phylogenetic analyses of cytochrome b sequences of malaria parasites and their avian hosts to assess the coevolutionary relationships between host and parasite lineages. Many lineages of avian malaria parasites have broad host distributions, which tend to obscure cospeciation events. The hosts of a single parasite or of closely related parasites were nonetheless most frequently recovered from members of the same host taxonomic family, more so than expected by chance. However, global assessments of the relationship between parasite and host phylogenetic trees, using Component and ParaFit, failed to detect significant cospeciation. The event-based approach employed by TreeFitter revealed significant cospeciation and duplication with certain cost assignments for these events, but host switching was consistently more prominent in matching the parasite tree to the host tree. The absence of a global cospeciation signal despite conservative host distribution most likely reflects relatively frequent acquisition of new hosts by individual parasite lineages. Understanding these processes will require a more refined species concept for malaria parasites and more extensive sampling of parasite distributions across hosts. If parasites can disperse between allopatric host populations through alternative hosts, cospeciation may not have a strong influence on the architecture of host-parasite relationships. Rather, parasite speciation may happen more often in conjunction with the acquisition of new hosts followed by divergent selection between host lineages in sympatry. Detailed studies of the phylogeographic distributions of hosts and parasites are needed to characterize these events.     

Population structure and the co-evolution between social parasites and their hosts

Co-evolutionary trajectories of host-parasite interactions are strongly affected by the antagonists' evolutionary potential, which in turn depends on population sizes as well as levels of recombination, mutation, and gene flow. Under similar selection pressures, the opponent with the higher evolutionary rate is expected to lead the co-evolutionary arms race and to develop local adaptations. Here, we use mitochondrial DNA sequence data and microsatellite markers to assess the amount of genetic variability and levels of gene flow in two host-parasite systems, each consisting of an ant social parasite--the European slavemaker Harpagoxenus sublaevis and the North American slavemaker Protomognathus americanus--and its two main host species. Our population genetic analyses revealed limited gene flow between individual populations of both host and parasite species, allowing for a geographic mosaic of co-evolution. In a between-system comparison, we found less genetic variability and more pronounced structure in Europe, where previous behavioural studies demonstrated strong local adaptation. Within the European host-parasite system, the larger host species Leptothorax acervorum exhibited higher levels of both genetic variability and gene flow, and previous field data showed that it is less affected by the social parasite H. sublaevis than the smaller host Leptothorax muscorum, which has genetically depleted and isolated populations. In North America, the parasite P. americanus showed higher levels of gene flow between sites, but overall less genetic diversity than its hyper-variable main host species, Temnothorax longispinosus. Interestingly, recent ecological and chemical studies demonstrated adaptation of P. americanus to local host populations, indicating the importance of migration in co-evolutionary interactions.     

Lack of Evidence for Cospeciation Between Retroelements and Their Hosts

Some literature is available on cospeciation and on reconstructing the phylogenetic relationships of retroelements, but relatively little consideration has been given to whether there is cospeciation between retroelements and their hosts. Here we address this problem in detail. We conclude that there is no significant evidence for cospeciation between retroelements and their hosts. This conclusion was reached by noting that the branching order of the two phylogenies was no more similar than would be expected by chance. Received: 18 February 1999 / Accepted: 1 October 1999     

The role of phylogeny and ecology in experimental host specificity: insights from a eugregarine-host system

The degree to which parasites use hosts is fundamental to host-parasite coevolution studies, yet difficult to assess and interpret in an evolutionary manner. Previous assessments of parasitism in eugregarine-host systems suggest high degrees of host specificity to particular host stages and host species; however, rarely have the evolutionary constraints on host specificity been studied experimentally. A series of experimental infections were conducted to determine the extent of host stadium specificity (larval vs. adult stage) and host specificity among 6 tenebrionid host species and 5 eugregarine parasite species. Eugregarines from all host species infected both the larva and adult stages of the host, and each parasite taxa colonized several host species (Tribolium spp. and Palorus subdepressus). Parasite infection patterns were not congruent with host phylogeny, suggesting that host phylogeny is not a significant predictor of host-parasite interactions in this system. However, the 2 host stages produced significantly different numbers of parasite propagules, indicating that ecological factors may be important determinants of host specificity in this host-parasite system. While field infections reflect extant natural infection patterns of parasites, experimental infections can demonstrate potential host-parasite interactions, which aids in identifying factors that may be significant in shaping future host-parasite interactions.