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.     

Phylogenetics and the future of helminth systematics

Phylogenetic systematics is a relatively new formal technique that increases the precision with which one can make direct estimates of the history of phylogenetic descent. These estimates are made in the form of phylogenetic trees, or cladograms. Cladograms may be converted directly into classifications or they may be used to test various hypotheses about the evolutionary process. More than 20 phylogenetic analyses of helminth groups have been published already, and these have been used to investigate evolutionary questions in developmental biology, biogeography, speciation, coevolution, and evolutionary ecology.     

Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification

Coevolution is thought to be especially important in diversification of obligate mutualistic interactions such as the one between yuccas and pollinating yucca moths. We took a three-step approach to examine if plant and pollinator speciation events were likely driven by coevolution. First, we tested whether there has been co-speciation between yuccas and pollinator yucca moths in the genus Tegeticula (Prodoxidae). Second, we tested whether co-speciation also occurred between yuccas and commensalistic yucca moths in the genus Prodoxus (Prodoxidae) in which reciprocal evolutionary change is unlikely. Finally, we examined the current range distributions of yuccas in relationship to pollinator speciation events to determine if plant and moth speciation events likely occurred in sympatry or allopatry. Co-speciation analyses of yuccas with their coexisting Tegeticula pollinator and commensalistic Prodoxus lineages demonstrated phylogenetic congruence between both groups of moths and yuccas, even though moth lineages differ in the type of interaction with yuccas. Furthermore, Yucca species within a lineage occur primarily in allopatry rather than sympatry. We conclude that biogeographic factors are the overriding force in plant and pollinator moth speciation and significant phylogenetic congruence between the moth and plant lineages is likely due to shared biogeography rather than coevolution.     

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.     

Algal switching among lichen symbioses

Lichens are intimate and long-term symbioses of algae and fungi. Such intimate associations are often hypothesized to have undergone long periods of symbiotic interdependence and coevolution. However, coevolution has not been rigorously tested for lichen associations. In the present study we compared the nuclear internal transcribed spacer (ITS) phylogenies of algal and fungal partners from 33 natural lichen associations to test two aspects of coevolution, cospeciation and parallel cladogenesis. Since statistically significant incongruence between symbiont phylogenies rejected parallel cladogenesis and minimized cospeciation events, we conclude that switching of highly selected algal genotypes occurs repeatedly among these symbiotic lichen associations.     

传粉细蛾与大戟科植物专性授粉的互惠共生体系

在已知的昆虫与植物所形成的专性授粉互惠共生体系中,榕树—榕小蜂、丝兰—丝兰蛾体系是经典实例,国内外学者已经从不同角度进行了大量的研究,为我们理解植物—传粉者互惠共生体系协同进化的机理和历史积累了宝贵的资料。近些年的研究发现鳞翅目细蛾科头细蛾属昆虫与大戟科植物之间也存在相似的协同进化关系。文章对国内外学者有关传粉细蛾与大戟科植物互惠共生协同进化的研究进行了整理。     

Host and parasite morphology influence congruence between host and parasite phylogenies

Comparisons of host and parasite phylogenies often show varying degrees of phylogenetic congruence. However, few studies have rigorously explored the factors driving this variation. Multiple factors such as host or parasite morphology may govern the degree of phylogenetic congruence. An ideal analysis for understanding the factors correlated with congruence would focus on a diverse host–parasite system for increased variation and statistical power. In this study, we focused on the Brueelia-complex, a diverse and widespread group of feather lice that primarily parasitise songbirds. We generated a molecular phylogeny of the lice and compared this tree with a phylogeny of their avian hosts. We also tested for the contribution of each host–parasite association to the overall congruence. The two trees overall were significantly congruent, but the contribution of individual associations to this congruence varied. To understand this variation, we developed a novel approach to test whether host, parasite or biogeographic factors were statistically associated with patterns of congruence. Both host plumage dimorphism and parasite ecomorphology were associated with patterns of congruence, whereas host body size, other plumage traits and biogeography were not. Our results lay the framework for future studies to further elucidate how these factors influence the process of host–parasite coevolution.     

Coevolution: a history of the macroevolutionary approach to studying host-parasite associations.

The year 1991 marked 100 yr of coevolution research. I have reviewed the first 90 yr of this history. Three chronological phases are apparent: recognition of predictable associations among hosts and their parasites; search for patterns of association and their underlying causes, emphasizing either correlated biogeographic patterns or correlated phylogenies; and development of objective and repeatable methodologies for reconstructing and interpreting these patterns of association. Von Ihering, an outspoken anti-Darwinian, was undoubtedly the first to recognize and make use of predictable host-parasite associations. Kellogg and Fahrenholz, however, had more profound influence on subsequent generations, but in different directions. Kellogg attempted to meld natural selection with speciation by isolation. He also considered host specificity a component of coevolution, important but variable. His work laid the foundation for future research concentrated on biogeographic interpretations of host-parasite relationships. This emphasis and Metcalf's failed attempts to provide adequate mechanisms for reconstructing phylogenies reduced the biogeographic approach to an empirical research program in the hands of Manter. Fahrenholz, on the other hand, exposed to a strong anti-Darwinian sentiment, emphasized the importance of strict host specificity. This led to Eichler's formulation of the first 3 coevolutionary rules and the conclusion that host specificity was not a component but the cause of coevolution and ultimately the tautology inherent in the phylogenetic approach. All had to rely on 1 assumption, that host and parasite phylogenies were reflected in the taxonomic hierarchy. Hennig criticized this assumption and provided a method whereby phylogenies are reconstructed independently. Brooks melded this new phylogenetic method (cladistics) with an equally new biogeographic method (vicariance biogeography), providing the foundations for the modern macroevolutionary approach to studying host-parasite associations.     

When phylogenetics met biogeography: Willi Hennig,Lars Brundin and the roots of phylogenetic and cladistic biogeography

Willi Hennig's (Beitr. Ent. 1960, 10, 15) Die Dipteren-Fauna von Neuseeland als systematisches und tiergeographisches Problem applied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns. The most important author who applied Hennig's phylogenetic biogeography was Lars Brundin, when analysing the phylogenetic relationships of two taxa of Chironomidae (Diptera) and using them to examine the biogeographic relationships of Australia, New Zealand, South America and South Africa. The relevance of Brundin's contribution was noted by several authors, as it began the cladistic or vicariance approach to biogeography, that implies the discovery of vicariance events shared by different monophyletic groups. Both phylogenetic and cladistic biogeography have a place in contemporary biogeography, the former for analysing taxon biogeography and the latter when addressing Earth or biota biogeography. The recent use of the term “phylogenetic biogeography” to refer to a posteriori methods of cladistic biogeography is erroneous and should be avoided.     

An effect of 16S rRNA intercistronic variability on coevolutionary analysis in symbiotic bacteria: molecular phylogeny of Arsenophonus triatominarum

The genes of ribosomal RNA are the most popular and frequently used markers for bacterial phylogeny and reconstruction of insect-symbiont coevolution. In primary symbionts, such as Buchnera and Wigglesworthia, genome economization leads to the establishment of a single copy of these sequences. In phylogenetic studies, they provide sufficient information and yield phylogenetic trees congruent with host evolution. In contrast, other symbiotic lineages (e.g., the genus Arsenophonus) carry a higher number of rRNA copies in their genomes, which may have serious consequences for phylogenetic inference. In this study, we show that in Arsenophonus triatominarum the degree of heterogeneity can affect reconstruction of phylogenetic relationships and mask possible coevolution between the symbiont and its host. Phylogenetic arrangement of individual rRNA copies was used, together with a calculation of their divergence time, to demonstrate that the incongruent 16S rDNA trees and low nucleotide diversity in the secondary symbiont could be reconciled with the coevolutionary scenario.     

Viral biogeography revealed by signatures in Sulfolobus islandicus genomes

Viruses are a driving force of microbial evolution. Despite their importance, the evolutionary dynamics that shape diversity in viral populations are not well understood. One of the primary factors that define viral population structure is coevolution with microbial hosts. Experimental models predict that the trajectory of coevolution will be determined by the relative migration rates of viruses and their hosts; however, there are no natural microbial systems in which both have been examined. The biogeographic distribution of viruses that infect Sulfolobus islandicus is investigated using genome comparisons among four newly identified, integrated, Sulfolobus spindle-shaped viruses and previously sequenced viral strains. Core gene sequences show a biogeographic distribution where viral genomes are specifically associated with each local population. In addition, signatures of host–virus interactions recorded in the sequence-specific CRISPR (clustered regularly interspaced short palindromic repeats) system show that hosts have interacted with viral communities that are more closely related to local viral strains than to foreign ones. Together, both proviral and CRISPR sequences show a clear biogeographic structure for Sulfolobus viral populations. Our findings demonstrate that virus–microbe coevolution must be examined in a spatially explicit framework. The combination of host and virus biogeography suggests a model for viral diversification driven by host immunity and local adaptation.     

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

Cospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and are not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data. We present a new functionality in the Mowgli software that bridges this gap. The user can provide geographic information on both the host and symbiont extant and ancestral taxa. Constraints in the reconciliation algorithm have been implemented to generate biologically realistic codiversification scenarios. We apply our method to the fig/fig wasp association and infer diversification scenarios that differ from reconciliations ignoring geographic information. In addition, we updated the reconciliation viewer SylvX to visualize ancestral character states on the phylogenetic trees and highlight parts of reconciliations that are geographically inconsistent when not accounting for geographic constraints. We suggest that the comparison of reconciliations obtained with and without such constraints can help solving ambiguities in the biogeographic histories of the partners. With the development of robust methods in historical biogeography, and the advent of next‐generation sequencing that leads to better‐resolved trees, a geography‐aware reconciliation method represents a substantial advance that is likely to be useful to researchers studying the evolution of biotic interactions and biogeography.     

Tectonic blocks and molecular clocks

Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.     

A data based parsimony method of cophylogenetic analysis

Phylogenies of closely interacting groups, such as hosts and parasites, are seldom completely congruent. Incongruence can arise from biologically meaningful differences in the histories of the two groups, or can be generated by artifactual differences that are merely the result of incorrect phylogenies with weakly supported nodes. We present a method that distinguishes between these sources of incongruence and identifies lineages that are responsible for significant differences between phylogenies. We use the logic of conditional combination in that we first test for statistically significant incongruence using the partition homogeneity test. Then we remove all possible combinations of taxa until a non-significant result of this test is achieved. Finally, we construct a 'combined evidence' phylogeny and then reposition the incongruent taxa. This method produces trees for final comparison using reconciliation methods, but it includes only as many incongruence events as can be statistically justified from the data sets. We apply this method to a host–parasite (gopher–louse) data set and identify many fewer incongruence events than do topology based analyses alone. Our method is broadly applicable to comparisons of phylogenies of interacting taxa, such as hosts and parasites, or mutualists. The method should also be useful for other problems involving comparisons of phylogenies, such as multiple gene trees or cladistic biogeography.     

EVOLUTIONARY CHARACTER ANALYSIS: TRACING CHARACTER CHANGE ON A CLADOGRAM

Abstract— There has been little formal discussion concerning character analysis in cladistics, even though characters and their character state trees are central to phylogenetic analyses. We refer to this field as Evolutionary Character Analysis. This paper defines the components of evolutionary character analysis: character state trees, transmodal characters, cladogram characters, attribute and character phylogenies; and the use of these components in phylogenetic inference and evolutionary studies. Character state trees and their effect on cladogram construction are discussed. A new method for numerically coding complex character state trees is described that further reduces the number of variables required to describe them. This method, ordinal coding, reduces the size of data matrices, and facilitates retrieval of state codes. This paper advocates the use of both biological evidence and evidence internal to the cladogram itself to construct character state trees (CSTs). We discuss general models of character evolution (morphocline analysis, Fitch minimum mutation model, etc.) and their role in forming CSTs. Character state trees formed with theories of character evolution are referred to as transmodal characters. These transmodal characters are contrasted with cladogram characters (Mickevich, 1982), and the place of each in a phylogenetic analysis is discussed. The method for determining cladogram characters is detailed with more complicated examples than found in previous publications. We advocate testing transmodal characters by comparing them with the resultant cladogram characters. This comparison involves transformation series analysis (TSA; Mickevich, 1982) which is viewed as an extension of reciprocal illumination. The TSA procedure and its place in hypothesis testing are reviewed. Tracing the evolution of characters interests both systematists and non-systematists alike. When character state trees (transmodal characters) are optimized on pre-existing phylogenies, character phylogenies and attribute phylogenies result. Attributes are defined as a feature that may or may not be homologous (i.e., ecological categories, plant hosts, etc.). We provide two illustrations of this approach, one involving the evolution of the anuran ear and another involving the coevolution of the butterfly Heliconius and its hostplants. Finally, the components of phylogenetic character analysis can be used to test more general evolutionary theories such as the biogenetic law and vicariance biogeography.     

An offer you cannot refuse: down‐regulation of immunity in response to a pathogen's retaliation threat

According to the Red Queen hypothesis, hosts and pathogens are engaged in an escalating coevolutionary arms race between resistance and virulence. However, the vast majority of symbionts colonize their hosts' mucosal compartments without triggering any immune response, resulting in durable commensal associations. Here, I propose a simple extension of previous mathematical models for antagonistic coevolution in which the host can mount a delayed immune response; in response, the symbiont can change its virulence following this activation. Even though the levels of virulence in both phases are assumed to be genetically determined, this simple form of plasticity can select for commensal associations. In particular, coevolution can result in hosts that do not activate their immune response, thus preventing phenotypically plastic pathogens from switching to a higher virulence level. I argue that, from the host's point of view, this state is analogous to the mafia behaviour previously described in avian brood parasites. More importantly, this study provides a new hypothesis for the maintenance of a commensal relationship through antagonistic coevolution.     

榕树及其传粉者研究综述

榕属植物（Ｆｉｃｕｓ）统称榕树,是热带森林中的一类关键种植物。榕树及其传粉者为协同进化的研究提供了丰富的实验材料,也是近年来国际上研究植物－昆虫相互作用的一个热点。本文对研究历史、植物、昆虫、传粉、产卵以及协同进化等方面的研究进展作了简要的介绍     

EVOLUTION OF THE HELIORNITHIDAE: RECIPROCAL ILLUMINATION BY MORPHOLOGY, BIOGEOGRAPHY AND DNA HYBRIDIZATION (AVES: GRUIFORMES)

Abstract— Finfoots (Heliornithidae) were chosen to test the possibility that there has been a dramatic reversal in a suite of morphological characters, intimated by an earlier phylogenetic reconstruction of Gruiformes based on DNA hybridization. There are three nodes where unstudied finfoots could stem from the existing reconstruction. The resulting alternate trees have largely exclusive implications for morphological character suite polarity, biogeography and fossil identifications. A new DNA hybridization study that includes all relevant taxa was intended to form the basis for independent evaluation of the trees, but it produced results that conflict with the earlier DNA study. So, instead, DNA trees were evaluated by their reproducibility and consensus with most-parsimonious trees, biogeography, paleontology and traditional classifications, I concur with traditional classifications that finfoots are monophyletic, and that Limpkin (Gruiformes: Aramidae) is the sister of cranes (Gruiformes: Gruidae). Limpkin is not supported as the sister of the Sungrebe ( Heliornis fulica ) or as a member of the Heliornithidae, as reported in the earlier DNA study. It is alarming that the gross lack of consensus with traditional characters and concomitant implications for character suite polarity in this case went unquestioned.     

Quantifying the phylodynamic forces driving papillomavirus evolution

The associations between pathogens and their hosts are complex and can result from a variety of evolutionary processes including codivergence, lateral transfer, or duplication. Papillomaviruses (PVs) are double-stranded DNA viruses ubiquitously present in mammals and are a suitable target for rigorous statistical tests of potential virus-host codivergence. We analyze the evolutionary dynamics of PV diversification by comparing robust phylogenies of PVs and their respective hosts using different statistical approaches to assess topological and branch-length congruence. Mammalian PVs segregated into four diverse major clades that overlapped to varying degrees in terms of their mammalian host lineages. The hypothesis that PVs and hosts evolved independently was globally rejected (P = 0.0001), although only 90 of 207 virus-host associations (43%) were significant in individual tests. Virus-host codivergence accounted roughly for one-third of the evolutionary events required to reconcile PV-host evolutionary histories. When virus-host associations were analyzed locally within each of the four viral clades, numerous independent topological congruencies were identified that were incompatible with respect to the global trees. These results support an evolutionary scenario in which early PV radiation was followed by independent codivergence between viruses within each of the major clades and their hosts. Moreover, heterogeneous groups of closely related PVs infecting non-related hosts suggest several interspecies transmission events. Our results argue thus for the importance of alternative events in PV evolution, in contrast to the prevailing opinion that these viruses show a high degree of host specificity and codivergence.     

The voice of historical biogeography

Historical biogeography is going through an extraordinary revolution concerning its foundations, basic concepts, methods, and relationships to other disciplines of comparative biology. There are external and internal forces that are shaping the present of historical biogeography. The external forces are: global tectonics as the dominant paradigm in geosciences, cladistics as the basic language of comparative biology and the biologist's perception of biogeography. The internal forces are: the proliferation of competing articulations, recourse to philosophy and the debate over fundamentals. The importance of the geographical dimension of life's diversity to any understanding of the history of life on earth is emphasized. Three different kinds of processes that modify the geographical spatial arrangement of the organisms are identified: extinction, dispersal and vicariance. Reconstructing past biogeographic events can be done from three different perspectives: (1) the distribution of individual groups (taxon biogeography) (2) areas of endemism (area biogeography), and (3) biotas (spatial homology). There are at least nine basic historical biogeographic approaches: centre of origin and dispersal, panbiogeography, phylogenetic biogeography, cladistic biogeography, phylogeography, parsimony analysis of endemicity, event-based methods, ancestral areas, and experimental biogeography. These nine approaches contain at least 30 techniques (23 of them have been proposed in the last 14 years). The whole practice and philosophy of biogeography depend upon the development of a coherent and comprehensive conceptual framework for handling the distribution of organisms and events in space.