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.     

A reconciliation analysis of host switching in plant-fungal symbioses

Plant-fungal symbioses include many familiar antagonistic and mutualistic associations and some model cases of coevolution. The relationship between coevolution at the different evolutionary scales has remained an open question. Widespread host specificity and documented host switches offer conflicting indications of what to expect from comparisons of plant and fungal phylogenies. This study sought to establish the role of plant phylogeny in determining fungal phylogeny and the relative contributions of codivergence and host switching by comparing tree topologies for 15 plant-fungal symbioses. Second it attempted to characterize the relationship between phylogenetic congruence and switching. Trees were estimated from published sequences and reconciliation analysis was applied in the form of cophylogeny mapping using "jungles". This provided an exhaustive account of all possible switches capable of reconciling two associated phylogenies. A continuum of cophylogenetic dynamics was identified, ranging from mostly codivergence (e.g., Exobasidium) to mostly switching, (e.g., Erysiphe). Surprisingly, congruent solutions do not necessarily have fewer switches when using cophylogeny mapping, but a significant negative relationship between congruence and the distance of switches proved to be a useful indicator. According to reconciliation analysis, the contribution of host phylogeny varies widely across plant-fungal symbioses, making host specificity and coadaptation poor indicators of macroevolutionary trends because they are necessary, but not sufficient, conditions.     

Sexual selection and the evolution of genital shape and complexity in water striders

Animal genitalia show two striking but incompletely understood evolutionary trends: a great evolutionary divergence in the shape of genitalic structures, and characteristic structural complexity. Both features are thought to result from sexual selection, but explicit comparative tests are hampered by the fact that it is difficult to quantify both morphological complexity and divergence in shape. We undertake a comparative study of multiple nongenitalic and male genital traits in a clade of 15 water strider species to quantify complexity and shape divergence. We show that genital structures are more complex and their shape more divergent among species than nongenital traits. Further, intromittent genital traits are more complex and have evolved more divergently than nonintromittent genital traits. More importantly, shape and complexity of nonintromittent genital traits show correlated evolution with indices of premating sexual selection and intromittent genital traits with postmating sexual selection, suggesting that the evolution of different components of genital morphology are shaped independently by distinct forms of sexual selection. Our quantitative results provide direct comparative support for the hypothesis that sexual selection is associated with morphological complexity in genitalic traits and highlight the importance of quantifying morphological shape and complexity, rather than size in studies of genital evolution.     

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.     

Cophylogenetic analysis of the relationship between anemonefish Amphiprion (Perciformes: Pomacentridae) and their symbiotic host anemones (Anthozoa: Actiniaria)

ABSTRACT

The association between anemonefish and anemone is a classical example of mutualism in coral reefs. Although mutualism is probably the key innovation that triggered the adaptive radiation of anemonefish into a wide range of habitats, the coevolutionary history between the groups has not been thoroughly tested in a phylogenetic framework. We examined the evolutionary history of the association via distance-based (Parafit and PACo) and event-based methods (Core-PA, Jane). Mitochondrial DNA sequences (COI mtDNA, Cytb, 16S rDNA and 12S rDNA) were used to reconstruct the phylogenies of tropical Amphiprion species and their host anemones by using maximum likelihood with best-fit models selected. Neither distance-based analyses nor event-based analyses revealed global significant congruence between the phylogenies of the hosts and the symbionts, and thus no evidence for coevolution between anemone-anemonefish. However, at the individual pair level, the fish showed some dependence on anemone hosts. Even though living in close association and benefiting from each other, the change of genetic composition of one species (anemonefish) does not always evolve in response to changes in the other (anemones). These findings expand our understanding of the pattern and the role of evolutionary events to allow a better prediction of the future of the anemonefish-anemone relationship.     

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.     

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.     

A nonparametric procedure associated with a clinically meaningful efficacy measure

Parametric methods such as analysis of (co)variance are commonly used for the analysis of data from clinical trials. They have the advantage of providing an easily interpretable measure of treatment efficacy such as a confidence interval for treatment difference. If there are doubts about the underlying distribution of the response variable, however, a nonparametric approach may be called for. The nonparametric approaches in such settings concentrate on hypothesis testing and are not typically used for providing easily interpretable measures of treatment efficacy. For comparing two treatments, we propose using a nonparametric measure based on the likelihood of observing a better response on one treatment than the other. The bootstrap method is used to construct a confidence interval for the treatment difference.     

Cophylogeny of the Ficus microcosm

The various mutualistic and antagonistic symbioses between fig trees (Ficus: Moraceae) and chalcid wasps comprise a community in microcosm. Phylogenetic estimates of figs and fig wasps show general topological correspondence, making the microcosm a model system for cophylogeny. Incongruence between phylogenies from associated organisms can be reconciled through a combination of evolutionary events. Cophylogeny mapping reconciles phylogenies by embedding an associate tree into a host tree, finding the optimal combinations of events capable of explaining incongruence and evaluating the level of codivergence. This review addresses the results of cophylogeny analysis concerning Ficus and discusses the plausibility of different evolutionary events. Five different associations encompassing fig-pollinator, fig-parasite and pollinator-parasitoid interactions are reconciled. The method improves on previous comparisons by employing 'jungles' to provide an exhaustive and quantitative analysis of cophylogeny. A jungle is a mechanism for inferring host switches and obtaining all potentially optimal solutions to the reconciliation problem. The results support the consensus that figs codiverge significantly with pollinators but not non-pollinators. However, pollinators still appear to have switched between hosts in contradiction to the traditional model of faithful codivergence. This emphasises the growing realisation that evolutionary transitions in the microcosm are more flexible than previously thought and host specificity is necessary but not sufficient for codivergence. The importance of sampling strategy is emphasised by the influence of taxon set on the fig-pollinator and fig-parasite jungles. Spurious significant results for fig-parasite and fig-parasitoid jungles indicate that the choice of congruence measure influences significance; the total number of events required to reconcile two trees ('total cost') is not a good measure of congruence when switches cannot be realistically weighted.     

The roles of cytoplasmic poly(A)-binding proteins in regulating gene expression: a developmental perspective.

Poly(A)-binding proteins (PABPs) are central to the regulation of messenger RNA (mRNA) translation and stability; however, the roles and contributions of different PABP family members in controlling gene expression are not yet fully understood. In this paper, the current state of knowledge of the different cytoplasmic PABP proteins and their function in animal cells will be summarised, with particular reference to their roles in development. Possible regulatory mechanisms and potential new roles for these proteins in the control of specific mRNAs are also highlighted.     

A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species

Evaluating trait correlations across species within a lineage via phylogenetic regression is fundamental to comparative evolutionary biology, but when traits of interest are derived from two sets of lineages that coevolve with one another, methods for evaluating such patterns in a dual‐phylogenetic context remain underdeveloped. Here, we extend multivariate permutation‐based phylogenetic regression to evaluate trait correlations in two sets of interacting species while accounting for their respective phylogenies. This extension is appropriate for both univariate and multivariate response data, and may use one or more independent variables, including environmental covariates. Imperfect correspondence between species in the interacting lineages can also be accommodated, such as when species in one lineage associate with multiple species in the other, or when there are unmatched taxa in one or both lineages. For both univariate and multivariate data, the method displays appropriate type I error, and statistical power increases with the strength of the trait covariation and the number of species in the phylogeny. These properties are retained even when there is not a 1:1 correspondence between lineages. Finally, we demonstrate the approach by evaluating the evolutionary correlation between traits in fig species and traits in their agaonid wasp pollinators. R computer code is provided.     

Parasite-mediated evolution of the functional part of the MHC in primates

The major histocompatibility complex (MHC) is a key model of genetic polymorphism, but the mechanisms underlying its extreme variability are debated. Most hypotheses for MHC diversity focus on pathogen-driven selection and predict that MHC polymorphism evolves under the pressure of a diverse parasite fauna. Several studies reported that certain alleles offer protection against certain parasites, yet it remains unclear whether variation in parasite pressure more generally covaries with allelic diversity and rates of molecular evolution of MHC across species. We tested this prediction in a comparative study of 41 primate species. We characterized polymorphism of the exon 2 of DRB region of the MHC class II. Our phylogenetic analyses controlled for the potential effects of neutral mutation rate, population size, geographic origin and body mass and revealed that nematode species richness associates positively with nonsynonymous nucleotide substitution rate at the functional part of the molecule. We failed to find evidence for allelic diversity being strongly related to parasite species richness. Continental distribution was a strong predictor of both allelic diversity and substitution rate, with higher values in Malagasy and Neotropical primates. These results indicate that parasite pressure can influence the different estimates of MHC polymorphism, whereas geography plays an independent role in the natural history of MHC.     

Fifty years of co‐evolution and beyond: integrating co‐evolution from molecules to species

Fifty years after Ehrlich and Raven's seminal paper, the idea of co‐evolution continues to grow as a key concept in our understanding of organic evolution. This concept has not only provided a compelling synthesis between evolutionary biology and community ecology, but has also inspired research that extends beyond its original scope. In this article, we identify unresolved questions about the co‐evolutionary process and advocate for the integration of co‐evolutionary research from molecular to interspecific interactions. We address two basic questions: (i) What is co‐evolution and how common is it? (ii) What is the unit of co‐evolution? Both questions aim to explore the heart of the co‐evolutionary process. Despite the claim that co‐evolution is ubiquitous, we argue that there is in fact little evidence to support the view that reciprocal natural selection and coadaptation are common in nature. We also challenge the traditional view that co‐evolution only occurs between traits of interacting species. Co‐evolution has the potential to explain evolutionary processes and patterns that result from intra‐ and intermolecular biochemical interactions within cells, intergenomic interactions (e.g. nuclear‐cytoplasmic) within species, as well as intergenomic interactions mediated by phenotypic traits between species. Research that bridges across these levels of organization will help to advance our understanding of the importance of the co‐evolutionary processes in shaping the diversity of life on Earth.     

Phylogenetic congruence of mealybugs and their primary endosymbionts

Tight interactions between unrelated organisms such as is seen in plant-insect, host-parasite, or host-symbiont associations may lead to speciation of the smaller partners when their hosts speciate. Totally congruent phylogenies of interacting taxa have not been observed often but a number of studies have provided evidence that various hemipteran insect taxa and their primary bacterial endosymbionts share phylogenetic histories. Like other hemipterans, mealybugs (Pseudococcidae) harbour multiple intracellular bacterial symbionts, which are thought to be strictly vertically inherited, implying codivergence of hosts and symbionts. Here, robust estimates of phylogeny were generated from four fragments of three nuclear genes for mealybugs of the subfamily Pseudococcinae, and a substantial fragment of the 16S-23S rDNA of their P-endosymbionts. Phylogenetic congruence was highly significant, with 75% of nodes on the two trees identical, and significant correlation of branch lengths indicated coincident timing of cladogenesis. It is suggested that the low level of observed incongruence was influenced by uncertainty in phylogenetic estimation, but evolutionary outcomes other than congruence, including host shifts, could not be rejected.     

A biogeographical perspective on ecological systems: some personal reflections

During my graduate studies, I characterized patterns of geographical distribution and taxonomic differentiation in birds of the West Indies, which suggested that species undergo phases of expansion and contraction similar to the taxon cycles that E. O. Wilson had described for Melanesian ants. Fieldwork in the early 1970s with George Cox confirmed that these phases were associated with variation in habitat distribution and abundance on individual islands, tying together local ecology and biogeography. Because taxon‐cycle stage was independent of taxonomic or ecological relationships among birds of the West Indies, George and I postulated that whether a species was in a phase of expansion or contraction reflected the outcome of coevolved relationships with antagonists, including pathogens. The taxon cycle concept had a cool reception initially, but subsequent phylogeographical analyses, beginning in the early 1990s with Eldredge Bermingham, provided a time scale that confirmed the relationship between taxon cycle stage and the relative age of the most recent population expansion. The discrete nature of islands allows one to visualize taxon cycles in island systems, but the principle should apply in a continental biota as well. The absence of strong phylogenetic effects in distribution and abundance is consistent with evolutionary lability caused by coevolutionary outcomes with specialized antagonists. Related species appear to compete for resources on a more‐or‐less equal footing across a broad range of environments, and their distribution at any particular time is likely to be determined primarily by their relationships with pathogens, among other antagonists. This model of distribution and abundance within a regional community is consistent with much of what we know about the interactions between pathogens and their host populations, but testing the model will require the development of a new research programme focused on endemic pathogen effects in natural communities.     

Culture and the evolution of human cooperation

The scale of human cooperation is an evolutionary puzzle. All of the available evidence suggests that the societies of our Pliocene ancestors were like those of other social primates, and this means that human psychology has changed in ways that support larger, more cooperative societies that characterize modern humans. In this paper, we argue that cultural adaptation is a key factor in these changes. Over the last million years or so, people evolved the ability to learn from each other, creating the possibility of cumulative, cultural evolution. Rapid cultural adaptation also leads to persistent differences between local social groups, and then competition between groups leads to the spread of behaviours that enhance their competitive ability. Then, in such culturally evolved cooperative social environments, natural selection within groups favoured genes that gave rise to new, more pro-social motives. Moral systems enforced by systems of sanctions and rewards increased the reproductive success of individuals who functioned well in such environments, and this in turn led to the evolution of other regarding motives like empathy and social emotions like shame.     

Extensive evolution analysis of the global chikungunya virus strains revealed the origination of CHIKV epidemics in Pakistan in 2016

Chikungunya virus (CHIKV) is a mosquito-borne virus that causes epidemics widely in the world especially in the tropical and subtropical regions. Phylogenetic analysis has found that the CHIKV lineages were associated with the spatial and temporal distributions, which were related to the virus adaption to the major mosquito species and their distributions. In this study, we reported the complete genome sequences of eight CHIKV isolates from the outbreak in Pakistan last year. Then we reviewed the evolutionary history using extensive phylogenetic analysis, analyzed lineage-specific substitutions in viral proteins, and characterized the spreading pathway of CHIKV strains including the Pakistani strains. The results showed that the Pakistani stains belonged to the ECSA.IOL sub-lineage and derived from India. The genetic properties of the Pakistani strains including the adaptive substitution to vectors were further characterized, and the potential risks from the occurrence of CHIKV infection in Pakistan were discussed. These results provided better understanding of CHIKV evolution and transmission in the world and revealed the possible origination of the CHIKV outbreak and epidemic in Pakistan, which would promote the disease prevention and control in the identified countries and territories with the history of CHIKV infections as well as new regions with potential risk of CHIKV outbreaks.

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Phylogenetic methodology for detecting protein interactions

Detecting protein-protein interactions and assigning proteins to functional complexes are key challenges of modern biology. The rise of genomics has lead to evidence that correlated patterns of presence/absence and/or fusing of proteins in any organism suggest these proteins interact. Unfortunately, methods based on such data work best with divergent genomes, whereas major sequencing efforts in vertebrates, for example, are yielding alignments of the same set of proteins sampled from the same set of taxa (species). Using vertebrate mitochondrial genomes to illustrate a novel method, we associate proteins based on vectors of their evolutionary tree edge (branch or internode) lengths. This approach is based on the expectation that molecular coevolution is greatest between proteins that interact in some way. Mitochondrial DNA-encoded proteins are associated into groups largely consistent with the complexes they come from. This association is apparently not due to the tree structure or mutation processes, leaving coevolution as the best explanation. We show that it is important that the tree used to derive the edge-length vector is estimated accurately in terms of both topology and edge lengths. Although more complex substitution models reduce systematic error, they also inflate stochastic error. This makes the use of less complex substitution models preferable in some circumstances. We describe a method to estimate correlations of pairwise evolutionary distances, which adjusts for non-independent correlations due to shared evolutionary history. Associations of proteins based on their edge-length vectors are visualized and assessed using a variety of hierarchical clustering and multidimensional scaling methods. New formula for estimating the fit of data to model, including the average percent standard deviation of distances on least squares trees, are presented. Use of edge-length vectors is compared and contrasted with correlated distance methods, correlated rates methods, and site-specific evidence of coevolution.     

The evolution of cultural evolution

Humans are unique in their range of environments and in the nature and diversity of their behavioral adaptations. While a variety of local genetic adaptations exist within our species, it seems certain that the same basic genetic endowment produces arctic foraging, tropical horticulture, and desert pastoralism, a constellation that represents a greater range of subsistence behavior than the rest of the Primate Order combined. The behavioral adaptations that explain the immense success of our species are cultural in the sense that they are transmitted among individuals by social learning and have accumulated over generations. Understanding how and when such culturally evolved adaptations arise requires understanding of both the evolution of the psychological mechanisms that underlie human social learning and the evolutionary (population) dynamics of cultural systems.     

The theory and application of plant competition models: an agronomic perspective

Many studies of plant competition have been directed towards understanding how plants respond to density in monocultures and how the presence of weeds affects yield in crops. In this Botanical Briefing, the development and current understanding of plant competition is reviewed, with particular emphasis being placed on the theory of plant competition and the development and application of mathematical models to crop-weed competition and the dynamics of weeds in crops. By consolidating the results of past research in this manner, it is hoped to offer a context in which researchers can consider the potential directions for future research in competition studies and its application to integrated weed management.