Pavel B. Klimov

Origin and higher-level relationships of psoroptidian mites (Acari: Astigmata: Psoroptidia): Evidence from three nuclear genes

Phylogenic relationships of the Psoroptidia, a group of primarily parasitic mites of vertebrates, were investigated based on sequences from three nuclear genes (4.2 kb aligned) sampled from 126 taxa. Several morphological classification schemes and a recent molecular analysis, suggesting that the group may not be monophyletic were statistically rejected by newly generated molecular data, and the results are robust under a range of analytical and partition strategies. Six families Psoroptidae, Lobalgidae (mammalian parasites), Pyroglyphidae (house dust mites and parasites inside feather calamus), Turbinoptidae (upper respiratory track parasites of birds), Psoroptoididae (downy feather mites), and Epidermoptidae (skin parasites of birds) form a well-supported monophyletic group (the epidermoptid-psoroptid complex). These relationships, recovered by combined and separate analyses of all gene partitions, were previously suspected based on some morphological evidence, but evidence has been dismissed as resulting from convergence based on similar parasitic ecologies. The existence of the epidermoptid-psoroptid complex and the statistical rejection of Sarcoptoidea (the morphology-based group joining all mammal-associated mites) indicate that current classification criteria, influenced as they are by host preferences, need to be reassessed for non-pterolichoid superfamilies. However, two of our findings remain sensitive to analytical methods and assumptions: (i) the families Heterocoptidae and Hypoderatidae as the first and second closest outgroups of Psoroptidia, respectively, and (ii) the superfamily Pterolichoidea (including Freyanoidea) forming a sister clade to the remaining psoroptidian superfamilies. Our findings suggest that (i) house dust mites (Pyroglyphidae: Dermatophagoidinae) originated from a parasitic ancestor within the core of Psoroptidia, violating a basic principle of evolution that it is virtually impossible for a permanent parasite to become free-living, and (ii) there were at least two shifts from presumably avian to mammalian hosts.

Multivariate Analysis of Morphological Variation in Two Cryptic Species of Sancassania (Acari: Acaridae) from Costa Rica

Abstract Populations of Sancassania mites were collected in Costa Rica from scarabaeid and passalid beetles and cultured. The populations proved to be reproductively incompatible due to postzygotic isolation and show 1.4% difference in domains 2 and 3 of the 28S nuclear rDNA gene, indicating the populations represent distinct species. Because the mites were virtually indistinguishable morphologically, 61 morphological characters of 50 females and 101 characters of 60 deutonymphs of the two species were analyzed. Traditional univariate morphometrics could not separate them. Multivariate analyses of variance (principal component and discriminant function) were used to interpret morphological differences between the two species in relation to factors that influence their morphology in a laboratory and field setting. Principal component analyses were done on size and shape as well as shape variables alone. The discriminant function analysis was done on a reduced subset of shape variables. In both cases, the shape analyses resulted in complete separation of the two species and the characters contributing strongly to the discrimination were used in formal description of the two species, Sancassania salasi sp. nov. and S. ochoai sp. nov. Although deutonymphs of S. salasi taken from field-collected beetles show a significantly smaller magnitude of size variation, they show significant deviation in shape compared with cultured deutonymphs of the same species, a potential problem for correlation of specimens of other Sancassania species from culture and nature. Characters that provide the strongest contribution to these intraspecific shape changes are, therefore, taxonomically unreliable.

Improved tRNA prediction in the American house dust mite reveals widespread occurrence of extremely short minimal tRNAs in acariform mites.

BackgroundAtypical tRNAs are functional minimal tRNAs, lacking either the D- or T-arm. They are significantly shorter than typical cloverleaf tRNAs. Widespread occurrence of atypical tRNAs was first demonstrated for secernentean nematodes and later in various arachnids. Evidence started to accumulate that tRNAs of certain acariform mites are even shorter than the minimal tRNAs of nematodes, raising the possibility that tRNAs lacking both D- and T-arms might exist in these organisms. The presence of cloverleaf tRNAs in acariform mites, particularly in the house dust mite genus Dermatophagoides, is still disputed.ResultsMitochondrial tRNAs of Dermatophagoides farinae are minimal, atypical tRNAs lacking either the T- or D-arm. The size (49-62, 54.4 ± 2.86 nt) is significantly (p = 0.019) smaller than in Caenorhabditis elegans (53-63, 56.3 ± 2.30 nt), a model minimal tRNA taxon. The shortest tRNA (49 nt) in Dermatophagoides is approaching the length of the shortest known tRNAs (45-49 nt) described in other acariform mites. The D-arm is absent in these tRNAs, and the inferred T-stem is small (2-3 bp) and thermodynamically unstable, suggesting that it may not exist in reality. The discriminator nucleotide is probably not encoded and is added postranscriptionally in many Dermatophagoides tRNAs.ConclusionsMitochondrial tRNAs of acariform mites are largely atypical, non-cloverleaf tRNAs. Among them, the shortest known tRNAs with no D-arm and a short and unstable T-arm can be inferred. While our study confirmed seven tRNAs in Dermatophagoides by limited EST data, further experimental evidence is needed to demonstrate extremely small and unusual tRNAs in acariform mites.

Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy.

With the proliferation of species-tree methods, empiricists now have to confront the daunting task of method choice. Such decisions might be made based on theoretical considerations alone. However, the messiness of real data means that theoretical ideals may not hold in practice (e.g., with convergence of complicated MCMC algorithms and computational times that limit analyses to small data sets). On the other hand, simplifying assumptions made by some approaches may compromise the accuracy of species-tree estimates. Here we examine the purported tradeoff between accuracy and computational simplicity for species-tree analysis, focusing on the different ways the approaches treat gene-tree uncertainty. By considering a diversity of species trees, as well as different sampling designs and total sampling efforts, we not only compare the accuracy of species-tree estimates across methods, but we also partition the variation in accuracy across factors to identify their relative importance. This analysis shows that although the method of analysis affects accuracy, other factors - namely, the history of species divergence and aspects of the sampling design - have a larger impact. Despite a full modeling of gene tree uncertainty (e.g., using a Bayesian framework), species-tree estimates may not be accurate, particularly for recent diversification histories. Nevertheless, we demonstrate how factors within the control of the empirical investigator (e.g., decisions about sampling) improve the accuracy of species tree estimates, and more so than the method of analysis. Lastly, with much of the attention on species-tree analyses focused on the discord among loci arising from the coalescent, this work also highlights a previously overlooked key determinant of species-tree accuracy for recent divergences - the level of genetic variation at a locus, which has important implications for improving species-tree estimates in practice.

Global phylogenetic structure of the hyperdiverse ant genus Pheidole reveals the repeated evolution of macroecological patterns

Adaptive radiations are of particular interest owing to what they reveal about the ecological and evolutionary regulation of biodiversity. This applies to localized island radiations such as Darwins finches, and also to rapid radiations occurring on a global scale. Here we analyse the macroevolution and macroecology of Pheidole, a famously hyperdiverse and ecologically dominant ant genus. We generate and analyse four novel datasets: (i) a robust global phylogeny including 285 Pheidole species, (ii) a global database on regional Pheidole richness in 365 political areas summarizing over 97 000 individual records from more than 6500 studies, (iii) a global database of Pheidole richness from 3796 local communities and (iv) a database of Pheidole body sizes across species. Analysis of the potential climate drivers of richness revealed that the patterns are statistically very similar across different biogeographic regions, with both regional and local richness associated with the same coefficients of temperature and precipitation. This similarity occurs even though phylogenetic analysis shows that Pheidole reached dominance in communities through serial localized radiations into different biomes within different continents and islands. Pheidole body size distributions have likewise converged across geographical regions. We propose these cases of convergence indicate that the global radiation of Pheidole is structured by deterministic factors regulating diversification and diversity.

Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae).

With the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference--species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates--a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.

MUSEUM SPECIMENS AND PHYLOGENIES ELUCIDATE ECOLOGY'S ROLE IN COEVOLUTIONARY ASSOCIATIONS BETWEEN MITES AND THEIR BEE HOSTS

Abstract Coevolutionary associations between hosts and symbionts (or parasites) are often reflected in correlated patterns of divergence as a consequence of limitations on dispersal and establishment on new hosts. Here we show that a phylogenetic correlation is observed between chaetodactylid mites and their hosts, the long-tongued bees; however, this association manifests itself in an atypical fashion. Recently derived mites tend to be associated with basal bee lineages, and vice versa, ruling out a process of cospeciation, and the existence of mites on multiple hosts also suggests ample opportunity for host shifts. An extensive survey of museum collections reveals a pattern of infrequent host shifts at a higher taxonomic level, and yet, frequent shifts at a lower level, which suggests that ecological constraints structure the coevolutionary history of the mites and bees. Certain bee traits, particularly aspects of their nesting behavior, provide a highly predictive framework for the observed pattern of host use, with 82.1% of taxa correctly classified. Thus, the museum survey and phylogenetic analyses provide a unique window into the central role ecology plays in this coevolutionary association. This role is apparent from two different perspectives—as (a) a constraining force evident in the historical processes underlying the significant correlation between the mite and bee phylogenies, as well as (b) by the highly nonrandom composition of bee taxa that serve as hosts to chaetodactylid mites.

Breaking out of biogeographical modules: range expansion and taxon cycles in the hyperdiverse ant genus Pheidole

Abstract Aim We sought to reconstruct the biogeographical structure and dynamics of a hyperdiverse ant genus, Pheidole, and to test several predictions of the taxon cycle hypothesis. Using large datasets on Pheidole geographical distributions and phylogeny, we (1) inferred patterns of biogeographical modularity (clusters of areas with similar faunal composition), (2) tested whether species in open habitats are more likely to be expanding their range beyond module boundaries, and (3) tested whether there is a bias of lineage flow from high‐ to low‐diversity areas. Location The Old World. Methods We compiled and jointly analysed a comprehensive database of Pheidole geographical distributions, the ecological affinities of different species, and a multilocus phylogeny of the Old World radiation. We used network modularity methods to infer biogeographical structure in the genus and comparative methods to evaluate the hypotheses. Results The network analysis identified eight biogeographical modules, and a suite of species with anomalous ranges that are statistically more likely to occur in open habitat, supporting the hypothesis that open habitats promote range expansion. Phylogenetic analysis shows evidence for a cascade pattern of colonization from Asia to New Guinea to the Pacific, but no ‘upstream’ colonization in the reverse direction. Main conclusions The distributions of Pheidole lineages in the Old World are highly modular, with modules generally corresponding to biogeographical regions inferred in other groups of organisms. However, some lineages have expanded their ranges across module boundaries, and these species are more likely to be adapted to open habitats rather than interior forest. In addition, there is a cascade pattern of dispersal from higher to lower diversity areas during these range expansions. Our findings are consistent with the taxon cycle hypothesis, although they do not rule out alternative interpretations.

Acarinaria in associations of apid bees (Hymenoptera) and chaetodactylid mites (Acari)

Acarinaria are specialised structures on the bodies of insects that harbour dispersing mites, providing a secure attachment place for the mites. The structures are best known among bees and wasps. Their presence remains enigmatic, however, since the associated mites often have negative or neutral effects on their hosts. A new hypothesis explaining the origin of the acarinarium as a specialised defence mechanism is proposed. In nests with partitions (as constructed by many bees and wasps), parasitic or cleptoparasitic mites are rarely found in all cells. They negatively interact only with host larvae developing in infested cells and apparently cannot disperse within the nest to attack others in the developing brood before bee emergence. Only when emerging bees break the partitions can the mites reach other hosts. We propose that acarinaria serve to concentrate unwanted mites, reducing the chance that they will disperse to other members of the brood as the infested host leaves the nest. Development of special mite pouches (acarinaria) by hymenopteran hosts presumably increases the likelihood that all mites will stay with the individual(s) with reduced fitness, thereby reducing their effect on other bees in the brood. This paper reviews the associations between chaetodactylid mites and long-tongued bees (Apidae and Megachilidae). Only apid bees (Apidae) have acarinaria; megachilid bees, which harbour species of Chaetodactylus that usually kill the bee larvae, do not possess acarinaria. The following associations involving previously undescribed acarinaria or mite species are reported: Achaetodactylus ceratinae (axillar acarinarium on Ceratina nigriceps); Roubikia latebrosa, sp. nov. (metasomal acarinarium on Tetrapedia sp.), Sennertia argentina (genital acarinarium on Xylocopa fimbriata), Sennertia devincta, sp. nov., Sennertia sayutara, sp. nov. (metasomal acarinaria on Ceratina (Zadontomerus) spp.), Sennertia lauta, sp. nov. and Sennertia ratiocinator, sp. nov. (incipient scutellar–metanotal acarinarium on Xylocopa (Zonohirsuta) spp.). In the latter case, the mites display a remarkable difference in the attachment sites between male and female hosts. In females, the mites are phoretic in a groove between the scutellum and metanotum (scutellar–metanotal acarinarium), whereas on males, mites attach to the hairs of the anterior scutum.

Conservation of the name Tyrophagus putrescentiae, a medically and economically important mite species (Acari: Acaridae)

ABSTRACT It was recently demonstrated that the taxonomic concept of Tyrophagus putrescentiae (Schrank, 1781), an ubiquitous, agriculturally and medically important mite species, involved two closely related species, and one of them was described as Tyrophagus communis Fan and Zhang, 2007. We show that the prevailing usage of the name T. putrescentiae includes almost exclusively one of these species, and this usage is not in taxonomic accord with the neotype designated by Robertson (1959). We propose that this neotype fixation for the species T. putrescentiae be set aside under Article 75.6 (ICZN, 1999) and a neotype consistent with the prevailing usage be designated. We verified the synonymy of T. putrescentiae (based on the new neotype) after examining the following taxa with extant types: Tyrophagus americanus (Banks, 1906), T. breviceps (Banks, 1906) n. syn, T. cocciphilus (Banks, 1906) n. syn, T. castellanii (Hirst, 1912), T. australasiae (Oudemans, 1916) (tentative synonymy), T. neotropicus Oudemans, 1917, T. amboinensis Oudemans (1925), T. nadinus (Lombardini, 1944), and T. communis Fan and Zhang, 2007, n. syn. For the taxon T. putrescentiae sensu Fan and Zhang (based on the neotype designated by Robertson) a new name is proposed, T. fanetzhangorum, n. sp. Lectotypes are designated for the following species: T. americanus, T. breviceps, T. cocciphilus, T. castellani, T. australasiae, T. neotropicus, T. amboinensis, and T. nadinus.