Phylogenetic relationships within terrestrial mites (Acari: Prostigmata, Parasitengona) inferred from comparative DNA sequence analysis of the mitochondrial cytochrome oxidase subunit I gene

Partial DNA and amino acid sequences translated from the mitochondrial cytochrome subunit I gene (408 bp) of 17 mite species have been used for analyzing the phylogenetic relationships within the terrestrial Parasitengona (Trombidia). Due to mutational saturation of the third codon position, only first and second codon positions and amino acid sequences were analyzed, applying neighbor-joining, maximum-parsimony, and maximum-likelihood tree-building methods. The reconstructed trees revealed similar topologies of taxa; however, the phylogenetic relationships could be convincingly resolved only within several trombidioid taxa. The proposed basic relationships within the Parasitengona, in particular those of Calyptostomatoidea, Smarididae, and Erythraeidae, were poorly supported in bootstrap tests. A comparison of the presented gene tree with a phylogenetic tree based upon traditional characters revealed only few contradictions in nodes only weakly supported by morphological data. The most astonishing result is the proposed early derivative position of Microtrombidiidae within the terrestrial Parasitengona.     

Extra-oral digestion and the problem of parasitism in Parasitengona mites (Acariformes)

An analysis of the extra-oral digestion in Parasitengona being a highly specialized group of Acariform mites is carried out from the viewpoint of functional morphology and ecology. The significance of the extra-oral digestion in the life strategy of these mites and their larval parasitism is also evaluated. The morphological pre-adaptations of this mode of feeding as well as its probable evolutionary consequences are demonstrated by an example of trombiculid mites (Trombiculidae). It is shown, in particular, that parasitism in general may be considered as a particular life scenario implying that the feeding preferences of the organism are evolutionary formed in a close association with other organisms, which provide a parasite with a feeding substrate mainly already prepared for utilization. Based on this assumption, all Parasitengona, including both larval and post-larval instars, irrespectively of the size of their potential victim, preferably should not be considered as parasites, but as micro-predators.     

Food-plant families of British insects and mites: the influence of life form and plant family

The dissimilarities between 107 British plant families with respect to the insect and mite species which feed on them were analysed using a principal co-ordinates analysis. The relationships between the plant families were strongly influenced by the plant life forms. Major groups were woody plants (trees and shrubs), aquatic plants and herbs. A wet to dry gradient was distinguished, as were evergreen plants, and early successional plant families with weeds and annuals. Taxonomically, plant families of the same order were closer together if they were predominantly of the same life form. Fagales and several orders of monocotyledons formed particularly clear groups. The three 'nearest neighbours' of each plant family based on the dissimilarities measures were listed. These provide some interesting, but conjectural, data on evolutionary aspects of plant families. This was illustrated briefly by the Cornaceae and Euphorbiaceae. The underlying progressive evolution of plants from woody species and wetter areas to herbs and annual plants of dry and cold places may be reflected by insect and mite food plant family associations.     

Morphology of Parasitengona mites (Acariformes: Parasitengona) and their possible evolutionary scenario

On the basis of the analysis of morphology and biology of representatives of the Parasitengona, mostly trombiculids, trombidiids and water mites, a new attempt is made to clarify probable evolutionary scenario in this group of the higher trombidiform mites (Actinedida). It is supposed that the very old ancestral group of terrestrial arachnids, having bite-sucking mouth-parts, poorly differentiated sac-like midgut and capability to extra-oral digestion, fed predatory on different small soil arthropods at all phases of the life cycle. They were small segmented orthotrichous homeomorphic arachnids at the rank of genus or family. The favorable feeding conditions of the adult phase have led to the small eggs rich in yolk and the small larva. The latter have led in turn to the necessity of intensive feeding at the larval stage to complete the ontogenesis. Further in evolution, this group gave rise at once to two or even more large paraphyletic branches. Most of them retained feeding on arthropods with transition of larvae to much more effective parasitic feeding provided with the additional specialization of the larval stage. This branch comprise divergently radiated paraphyletic terrestrial and secondary-water water mites each having long course of evolution resulted in the recent groups of Calyptostomatoidea, Erythraeoidea, Trombidioidea and several superfamilies of water mites. Another branch of the ancestral Parasitengona has followed the way of adaptation of larvae to feeding on vertebrates, which were being attacked by the larvae in the environment of pasture. The parasitism on vertebrates has lead to several radical specializations of these mites and their significant evolutionary progress. At the same time, the similar ontogenetic dynamics, as well as synchronous reduction of particular developmental stages in all parasitengones, inevitably indicate the monophyletic origin of the whole branch of Parasitengona with Pterygosomatidae as the most probable sister group.     

Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement

During evolution, organisms have gained functional complexity mainly by modifying and improving existing functioning systems rather than creating new ones ab initio. Here we explore the interplay between two processes which during evolution have had major roles in the acquisition of new functions: gene duplication and protein domain rearrangements. We consider four possible evolutionary scenarios: gene families that have undergone none of these event types; only gene duplication; only domain rearrangement, or both events. We characterize each of the four evolutionary scenarios by functional attributes. Our analysis of ten fungal genomes indicates that at least for the fungi clade, species significantly appear to gain complexity by gene duplication accompanied by the expansion of existing domain architectures via rearrangements. We show that paralogs gaining new domain architectures via duplication tend to adopt new functions compared to paralogs that preserve their domain architectures. We conclude that evolution of protein families through gene duplication and domain rearrangement is correlated with their functional properties. We suggest that in general, new functions are acquired via the integration of gene duplication and domain rearrangements rather than each process acting independently.     

Taxonomic,geographic and seasonal distribution of thelytokous parthenogenesis in the Desmonomata (Acari: Oribatida)

Based on sex-ratio analysis, thelytokous parthenogenesis is shown to be widespread in the mite taxon Desmonomata (Nothroidea sensu lato), with four of the seven families completely thelytokous and a fifth nearly so. Monthly samples from populations in central New York State, Japan, and Canada, representing 22 species in five families, indicate that sex-ratios are constantly highly femalebiased, with thelytoky probably being obligate. Similar sex-ratios regardless of provenance show that there is no geographic parthenogenesis phenomenon. Our data suggest that thelytoky is not an adaptation for particular environments, that this reproductive mode is not recent in these mites, and that speciation and evolutionary radiation probably occurred in the absence of biparental reproduction.     

RecPD: A Recombination-aware measure of phylogenetic diversity

A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) is assessing their diversity and distribution among a sample of individuals. Accurate assessments of these patterns are essential for linking features to traits or outcomes of interest and understanding their functional impact. Consequently, it is of crucial importance that the measures employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard measures used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity statistic for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive several related measures from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably reconstructs feature evolutionary histories under diverse recombination and loss scenarios. We then applied RecPD in two diverse real-world scenarios including a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and growth phenotypes of the Pseudomonas genus and demonstrate that prevalence is an inadequate measure that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.     

Spatial and Temporal Simulation of Human Evolution. Methods,Frameworks and Applications

Analyses of human evolution are fundamental to understand the current gradients of human diversity. In this concern, genetic samples collected from current populations together with archaeological data are the most important resources to study human evolution. However, they are often insufficient to properly evaluate a variety of evolutionary scenarios, leading to continuous debates and discussions. A commonly applied strategy consists of the use of computer simulations based on, as realistic as possible, evolutionary models, to evaluate alternative evolutionary scenarios through statistical correlations with the real data. Computer simulations can also be applied to estimate evolutionary parameters or to study the role of each parameter on the evolutionary process. Here we review the mainly used methods and evolutionary frameworks to perform realistic spatially explicit computer simulations of human evolution. Although we focus on human evolution, most of the methods and software we describe can also be used to study other species. We also describe the importance of considering spatially explicit models to better mimic human evolutionary scenarios based on a variety of phenomena such as range expansions, range shifts, range contractions, sex-biased dispersal, long-distance dispersal or admixtures of populations. We finally discuss future implementations to improve current spatially explicit simulations and their derived applications in human evolution.     

Parasitism of mosquitoes (Diptera: Culicidae) by larval mites (Acari: Parasitengona) in Adelaide, South Australia

Larval mites (Acari) from the cohort Parasitengona were collected from adult female mosquitoes captured in Adelaide, South Australia, from 1997 to 2000. Larvae from three families were identified: Arrenuridae, Hydryphantidae and Erythraeidae. Arrenurid larvae were associated with mosquitoes that use ground pools for larval habitat, while hydryphantids were associated with tree-hole and container-breeding species. Only a single erythraeid record was made. The overall prevalence of parasitism was very low (0.27% of 19 280 mosquitoes) and ranged from 0 to 5.6% for the 16 mosquito species collected. New mite–host records are presented.     

Exceptions to the one:one relationship between African fig trees and their fig wasp pollinators: possible evolutionary scenarios

Abstract. The mutualistic breeding system involving fig trees (Moraceae, Ficus ) and fig wasps (Hymenoptera, Chalcidoidea, Agaoninae) would appear so specialized that one may wonder at the evolutionary processes that could be responsible for the existence of about 750 species-specific associations. In this paper we present data concerning two cases of species specificity breakdown between African fig trees and fig wasps. We then analyse the possible evolutionary scenarios which could be responsible, as well as the possible evolutionary outcomes of the observed situations. Our analyses range in scale from continental to habitats, and fig crops to individual figs (syconia). Habitat shifts and ecological barriers seem to be the more likely explanations for the evolution of novel fig tree-fig wasp associations, but sympatric and parapatric scenarios cannot be ruled out.     

Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor

While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that these proteins are homologous to several families of unknotted membrane proteins. This allows us to directly investigate the evolution of the slipknot motif. Based on our comprehensive analysis of 17 distantly related protein families, we have found that slipknotted and unknotted proteins share a common structural motif. Furthermore, this motif is conserved on the sequential level as well. Our results suggest that, regardless of topology, the proteins we studied evolved from a common unknotted ancestor single domain protein. Our phylogenetic analysis suggests the presence of at least seven parallel evolutionary scenarios that led to the current diversity of proteins in question. The tools we have developed in the process can now be used to investigate the evolution of other repeated-domain proteins.     

Evolutionary history as a driver of ecological networks: a case study of plant–hummingbird interactions

Multiple factors drive species interactions in ecological networks, such as morphological barriers, spatio–temporal distribution, abundances and evolutionary histories of species. Novel methods are making it possible to evaluate the relative importance of each of these drivers. However, the lack of appropriate methods has prevented evaluating the extent to which interaction networks are shaped by species’ evolutionary histories. This study includes the evolutionary histories of species among the potential drivers of interactions, allowing the comparative analysis of its importance in structuring ecological networks. We hypothesized different possible phylogenetic scenarios to predict frequencies of interactions between species by combining concepts from the fields of ecological networks and ecophylogenetics. The usage of these scenarios is illustrated in a plant–hummingbird interaction network database from the Atlantic Forest, southeastern Brazil. We first evaluated which phylogenetic hypotheses better predict the observed network; subsequently, we evaluated the relative importance of species evolutionary histories, abundances, and matching on species morphologies and phenologies as drivers of their frequencies of interactions. The results suggest that the evolutionary histories of hummingbirds are more important than the species abundances in structuring the studied plant–hummingbird network but less important than the morphological and phenological matching among species. The approach developed here offers the potential to advance our understanding of the multiple factors structuring ecological networks.     

Comparative ultrastructure of coxal glands in unfed larvae of Leptotrombidium orientale (Schluger, 1948) (Trombiculidae) and Hydryphantes ruber (de Geer, 1778) (Hydryphantidae)

Coxal glands of unfed larvae Leptotrombidium orientale (Schluger, 1948) (Trombiculidae), a terrestrial mite parasitizing vertebrates, and Hydryphantes ruber (de Geer, 1778) (Hydryphantidae), a water mite parasitizing insects were studied using transmission electron microscopy. In both species, the coxal glands are represented by a paired tubular organ extending on the sides of the brain from the mouthparts to the frontal midgut wall and are formed of the cells arranged around the central lumen. As in other Parasitengona, the coxal glands are devoid of a proximal sacculus. The excretory duct, joining with ducts of the prosomal salivary glands constitutes the common podocephalic duct, opening into the subcheliceral space. The coxal glands of L. orientale are composed of a distal tubule with a basal labyrinth, an intermediate segment without labyrinth, and a proximal tubule bearing tight microvilli on the apical cell surface and coiled around the intermediate segment. The coxal glands of H. ruber mainly consist of the uniformly organized proximal tubule with apical microvilli of the cells lacking the basal labyrinth. This tubule shows several loops running backward and forward in a vertical plane on the side of the brain. In contrast to L. orientale , larvae of H. ruber reveal a terminal cuticular sac/bladder for accumulation of secreted fluids. Organization of the coxal glands depends on the ecological conditions of mites. Larvae of terrestrial L. orientale possess distal tubule functioning in re‐absorption of ions and water. Conversely, water mite larvae H. ruber need to evacuate of the water excess, so the filtrating proximal tubule is prominent.     

Co-evolution between ectoparasites and their insect hosts: a simulation study of a damselfly–water mite interaction

1. A simulation model investigating the co‐evolution of water mites infesting their aquatic insect hosts during emergence is presented. The model is based on field and experimental studies of the ectoparasitic water mite Arrenurus cuspidator and the damselfly Coenagrion puella. 2. Three scenarios were studied: (1) Only the host was allowed to evolve timing of emergence, while the timing of the parasites' infestation opportunity was held constant. (2) Both host and parasite were allowed to evolve. (3) Only the parasite's timing was allowed to evolve, while the host was constrained completely. 3. In the first two scenarios, parasite abundances decreased in the course of evolution and reached values well below those found in the field, whereas in the third scenario, parasite abundances were maintained at a level close to that found in the field. In the second scenario (co‐evolution), the host seemed to be the leader in the evolutionary race. 4. It is concluded that water mite parasitism is capable of shaping emergence patterns in aquatic insects and, despite the same life‐cycle length for host and parasite, the parasite evolves fast enough to shape its hatching pattern to match the emergence pattern of its host.     

Reproduction of ectoparasitic mites in a coevolved system: Varroa spp.—Eastern honey bees,Apis cerana

Parasite host shifts can impose a high selective pressure on novel hosts. Even though the coevolved systems can reveal fundamental aspects of host–parasite interactions, research often focuses on the new host–parasite relationships. This holds true for two ectoparasitic mite species, Varroa destructor and Varroa jacobsonii, which have shifted hosts from Eastern honey bees, Apis cerana, to Western honey bees, Apis mellifera, generating colony losses of these pollinators globally. Here, we study infestation rates and reproduction of V. destructor and V. jacobsonii haplotypes in 185 A. cerana colonies of six populations in China and Thailand to investigate how coevolution shaped these features. Reproductive success was mostly similar and low, indicating constraints imposed by hosts and/or mite physiology. Infestation rates varied between mite haplotypes, suggesting distinct local co‐evolutionary scenarios. The differences in infestation rates and reproductive output between haplotypes did not correlate with the virulence of the respective host‐shifted lineages suggesting distinct selection scenarios in novel and original host. The occasional worker brood infestation was significantly lower than that of drone brood, except for the V. destructor haplotype (Korea) from which the invasive lineage derived. Whether mites infesting and reproducing in atypical intraspecific hosts (i.e., workers and queens) actually predisposes for and may govern the impact of host shifts on novel hosts should be determined by identifying the underlying mechanisms. In general, the apparent gaps in our knowledge of this coevolved system need to be further addressed to foster the adequate protection of wild and managed honey bees from these mites globally.     

Structural evolution of the protein kinase-like superfamily

The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all three superkingdoms of life. We used a carefully constructed structural alignment of selected kinases as the basis for a study of the structural evolution of the protein kinase-like superfamily. The comparison of structures revealed a "universal core" domain consisting only of regions required for ATP binding and the phosphotransfer reaction. Remarkably, even within the universal core some kinase structures display notable changes, while still retaining essential activity. Hence, the protein kinase-like superfamily has undergone substantial structural and sequence revision over long evolutionary timescales. We constructed a phylogenetic tree for the superfamily using a novel approach that allowed for the combination of sequence and structure information into a unified quantitative analysis. When considered against the backdrop of species distribution and other metrics, our tree provides a compelling scenario for the development of the various kinase families from a shared common ancestor. We propose that most of the so-called "atypical kinases" are not intermittently derived from protein kinases, but rather diverged early in evolution to form a distinct phyletic group. Within the atypical kinases, the aminoglycoside and choline kinase families appear to share the closest relationship. These two families in turn appear to be the most closely related to the protein kinase family. In addition, our analysis suggests that the actin-fragmin kinase, an atypical protein kinase, is more closely related to the phosphoinositide-3 kinase family than to the protein kinase family. The two most divergent families, alpha-kinases and phosphatidylinositol phosphate kinases (PIPKs), appear to have distinct evolutionary histories. While the PIPKs probably have an evolutionary relationship with the rest of the kinase superfamily, the relationship appears to be very distant (and perhaps indirect). Conversely, the alpha-kinases appear to be an exception to the scenario of early divergence for the atypical kinases: they apparently arose relatively recently in eukaryotes. We present possible scenarios for the derivation of the alpha-kinases from an extant kinase fold.     

Sialidase-like Asp-boxes: sequence-similar structures within different protein folds

Sequence similarity is the most common measure currently used to infer homology between proteins. Typically, homologous protein domains show sequence similarity over their entire lengths. Here we identify Asp box motifs, initially found as repeats in sialidases and neuraminidases, in new structural and sequence contexts. These motifs represent significantly similar sequences, localized to beta hairpins within proteins that are otherwise different in sequence and three-dimensional structure. By performing a combined sequence- and structure-based analysis we detect Asp boxes in more than nine protein families, including bacterial ribonucleases, sulfite oxidases, reelin, netrins, some lipoprotein receptors, and a variety of glycosyl hydrolases. Although the function common to each of these proteins, if any, remains unclear, we discuss possible functions of Asp boxes on the basis of previously determined experimental results and discuss different evolutionary scenarios for the origin of Asp-box containing proteins.     

The Concept of Monophyly: A Speculative Essay

The concept of monophyly is central to much of modern biology. Despite many efforts over many years, important questions remain unanswered that relate both to the concept itself and to its various applications. This essay focuses primarily on four of these: i) Is it possible to define monophyly operationally, specifically with respect to both the structures of genomes and at the levels of the highest phylogenetic categories (kingdoms, phyla, classes)? ii) May the mosaic and chimeric structures of genomes be sufficiently important factors in phylogeny that situations exist in which the concept may not be applicable? iii) In the history of life on earth were there important groups of organisms that probably had polyphyletic, rather than monophyletic, origins? iv) Does the near universal search for monophyletic origins of clades lead, on occasion, to both undesirable narrowing of acceptable options for development of evolutionary scenarios and sometimes actual omission from consideration of less conventional types of both data and modes of thought, possibly at the expense of biological understanding? Three sections in the essay consider possible answers to these questions: i) A reassessment is made of major features of both the concept and some of its applications. Recent research results make it seem improbable that there could have been single basal forms for many of the highest categories of evolutionary differentiation (kingdoms, phyla, classes). The universal tree of life probably had many roots. Facts contributing to this perception include the phylogenetically widespread occurrences of: horizontal transfers of plasmids, viral genomes, and transposons; multiple genomic duplications; the existence and properties of large numbers of gene families and protein families; multiple symbioses; broad-scale hybridizations; and multiple homoplasys. Next, justifications are reassessed for the application of monophyletic frameworks to two major evolutionary developments usually interpreted as having been monophyletic: ii) the origins of life; and iii) the origins of the vertebrate tetrapods. For both cases polyphyletic hypotheses are suggested as more probable than monophyletic hypotheses. Major conclusions are, as answers to the four questions posed above: probably not, yes, yes, and yes.     

Climate change effects on walnut pests in California

Increasing temperatures are likely to impact ectothermic pests of fruits and nuts. This paper aims to assess changes to pest pressure in California's US$0.7 billion walnut industry due to recent historic and projected future temperature changes. For two past (1950 and 2000) and 18 future climate scenarios (2041–2060 and 2080–2099; each for three General Circulation Models and three greenhouse gas emissions scenarios), 100 years of hourly temperature were generated for 205 locations. Degree‐day models were used to project mean generation numbers for codling moth (Cydia pomonella L.), navel orangeworm (Amyelois transitella Walker), two‐spotted spider mite (Tetranychus urticae Koch), and European red mite (Panonychus ulmi Koch). In the Central Valley, the number of codling moth generations predicted for degree days accumulated between April 1 and October 1 rose from 2–4 in 1950 to 3–5 among all future scenarios. Generation numbers increased from 10–18 to 14–24 for two‐spotted spider mite, from 9–14 to 14–20 for European red mite, and from 2–4 to up to 5 for navel orangeworm. Overall pest pressure can thus be expected to increase substantially. Our study did not include the possibility of higher winter survival rates, leading to higher initial pest counts in spring, or of extended pest development times in the summer, factors that are likely to exacerbate future pest pressure. On the other hand, initiation of diapause may prevent an extension of the season length for arthropods, and higher incidence of heat death in summer may constrain pest population sizes. More information on the impact of climate change on complex agroecological food webs and on the response of pests to high temperatures is needed for improving the reliability of projections.     

Nonrandom extinction leads to elevated loss of angiosperm evolutionary history

The phylogenetic clustering of extinction may jeopardize the existence of entire families and genera, which can result in elevated reductions of evolutionary history (EH), trait diversity, and ecosystem functioning. Analyses of globally threatened birds and mammals suggest current extinction threats will result in a much higher loss of EH than random extinction scenarios, while the analyses of the taxonomical distribution of regionally rare plants find the opposite pattern. The disproportionately high number of rare plant species within species-rich families potentially suggests that lower losses of plant EH will be sustained than expected under random extinction. We show that at a global scale, this is not the case. Species-poor (especially monotypic) angiosperm families are more often at risk of extinction than expected. Because these high-risk species-poor families are as evolutionarily distinct as other families, the expected family-level EH plausibly lost in the next 100 years exceeds that predicted from random extinction by up to approximately 1165 million years.