Mitochondrial differentiation in a polymorphic land snail: evidence for Pleistocene survival within the boundaries of permafrost

The genetic differentiation of populations having colonized formerly unsuitable habitats after the Pleistocene glaciations depends to a great extent on the speed of expansion. Slow dispersers maintain their refugial diversity whereas fast dispersal leads to a reduction of diversity in the newly colonized areas. During the Pleistocene, almost the entire current range of the land snail Arianta arbustorum has repeatedly been covered with ice or been subjected to permafrost. Owing to the low potential for dispersal of land snails, slow (re)colonization of the wide range from southern refugia can be excluded. Alternatively, fast, passive dispersal from southern refugia or survival in and expansion from multiple refugia within the area subjected to permafrost may account for the current distribution. To distinguish between these scenarios we reconstructed a phylogeography based on the sequences of a fragment of the cytochrome oxidase I from 133 individuals collected at 45 localities and analysed the molecular variance. Seventy-five haplotypes were found that diverged on average at 7.52% of positions. This high degree of diversity suggests that A. arbustorum is an old species in which the population structure, isolation and the hermaphroditic nature have reduced the probability of lineage extinction. The genetic structure was highly significant with the highest variance partition found among regions. Geographic distance and mitochondrial differentiation were not congruent. Lineages had overlapping ranges. The clear genetic differentiation and the patchy pattern of haplotype distribution suggest that colonization of formerly unsuitable habitats was mainly achieved from multiple populations from within the permafrost area.     

Multiplication of the agent of X-disease in a non-vector leafhopper Macrostelesfascifrons

The relative titre of the causal agent of X-disease of stone fruits in the non-vector leafhopper Macrosteles fascifrons was tested by injecting dilutions of M. fascifrons extracts into non-infective Colladonus montanus leafhopper vectors. The recipient C. montanus were fed on celery test plants which were then observed for X-disease symptoms. M. fascifrons were assayed at various intervals for up to 37 days after they were fed on X-diseased celery or injected with infectious extracts of the X-agent. Infectivity was detected in M. fascifrons only after 25 or 37 days in separate trials. Whole body extracts but not extracts from detached heads of M. fascifrons that had fed on X-diseased celery were infectious, whereas extracts prepared from the heads of M. fascifrons previously injected with X-agent extracts were infectious. This infectivity was retained for up to four serial passages in M. fascifrons. Electron microscopy of M. fascifrons that had been injected with extracts of the X-disease agent revealed mycoplasma-like organisms (MLO) only intercellularly and appressed to various organs in the haemocoele. No MLO were observed in uninjected M. fascifrons or those injected with extracts from non-infectious C. montanus. These results suggest that, despite multiplication of the X-agent in vivo. barriers in the gut and salivary glands prevent its transmission to plants by M. fascifrons.     

The effect of introducing aphid-pathogenic Entomophthoraceae into field populations of Aphis fabae

During two warm, dry seasons (1975 and 1976) aphid-pathogenic species of Entomophthoraceae introduced into Aphis fabae populations on field beans established briefly but failed to spread. In cool moist seasons (1977 and 1978), the fungi, principally Erynia neoaphidis and Neozygites fresenii, spread more rapidly in treated than untreated plots. In 1977, the maximum aphid population in plots treated with fungi reached a mean of 9000/plant on 19 July compared with 16 000/plant 1 wk later in untreated plots. The corresponding yield of beans in treated plots was twice that in untreated plots though only half that in plots kept free of aphids with pirimicarb. In two experiments in 1978, the maximum aphid population in treated areas was 700/plant, half that in untreated areas and 1 to 2 wk earlier. Yields from treated plots, however, were not significantly different from those from untreated plots. In nature, the fungi attack A. fabae populations in England only after they have become damaging, partly because fungal inoculum is sparse when the aphid population is small.     

Phylogenetic signal and its decay in mitochondrial SSU and LSU rRNA gene fragments of Anisoptera

The phylogeny of Anisoptera, dragonflies in the strict sense, has proven to be notoriously difficult to resolve. Based on morphological characters, several recent publications dealing with the phylogeny of dragonflies proposed contradicting inter- and intrafamily relationships. We explored phylogenetic information content of mitochondrial large-subunit (LSU) and small-subunit (SSU) ribosomal gene fragments for these systematic problems. Starting at published universal primers, we developed primer sets suitable for amplifying large parts of the LSU and SSU rRNA genes within dragonflies. These fragments turned out to harbor sufficient phylogenetic information to satisfyingly resolve intrafamily relationships, but they contain insufficient phylogenetic structure to permit reliable conclusions about several interfamily relationships. We demonstrate that decay of phylogenetic signal progresses from intrafamily to interfamily to outgroup relationships and is correlated with an increase of genetic distances. As expected, signal decay is most pronounced in fast-changing sites. Additionally, base composition among fast-changing sites significantly deviates from the expected homogeneity. Homogeneity of base composition among all included taxa was restored only after removing fast-changing sites from the data set. The molecular data tentatively support interfamily relationships proposed by the most recent publication based on morphological characters of fossil and extant dragonflies.     

Cytotaxonomic studies in the Adiantum caudatum complex of Africa and Asia

Study of meiosis in synthesized hybrids has permitted a genome analysis to be carried out with respect to the holotype of A. indicum Ghatak, 4x, originally found wild near Calcutta. The two differentiated diploids from which A. indicum , 4x, seems to have arisen are represented in the analysis by A. zollingeri from Ceylon and by two strains of an Indian diploid provisionally designated A. incisum sens. lat. 2x. Supplementary information excluding an autopolyploid origin for A. indicum is provided by hybrids between A. indicum 4x and an unrelated tetraploid, A. malesianum Ghatak. Ecological information is supplied for the material of A. zollingeri , indicating that it occupies a specialized habitat which might be found in India if search is made in the right kind of territory. A. incisum 2x is shown to be much more widespread and to be present in hill country, or occasionally in lowlands, from the Himalayas to South India inclusive. It contains a number of genetically determined biotypes differing slightly in morphology but behaving as members of one species when combined into hybrids. Further morphological information and a revised key for separating the specimens used in the investigation is provided in an Appendix.     

Towards an 18S phylogeny of hexapods: accounting for group-specific character covariance in optimized mixed nucleotide/doublet models

The phylogenetic diversification of Hexapoda is still not fully understood. Morphological and molecular analyses have resulted in partly contradicting hypotheses. In molecular analyses, 18S sequences are the most frequently employed, but it appears that 18S sequences do not contain enough phylogenetic signals to resolve basal relationships of hexapod lineages. Until recently, character interdependence in these data has never been treated seriously, though possibly accounting for the occurrence of biased results. However, software packages are readily available which can incorporate information on character interdependence within a Bayesian approach. Accounting for character covariation derived from a hexapod consensus secondary structure model and applying mixed DNA/RNA substitution models, our Bayesian analysis of 321 hexapod sequences yielded a partly robust tree that depicts many hexapod relationships congruent with morphological considerations. It appears that the application of mixed DNA/RNA models removes many of the anomalies seen in previous studies. We focus on basal hexapod relationships for which unambiguous results are missing. In particular, the strong support for a “Chiastomyaria” clade (Ephemeroptera+Neoptera) obtained in Kjer's [2004. Aligned 18S and insect phylogeny. Syst. Biol. 53, 1–9] study of 18S sequences could not be confirmed by our analysis. The hexapod tree can be rooted with monophyletic Entognatha but not with a clade Ellipura (Collembola+Protura). Compared to previously published contributions, accounting for character interdependence in analyses of rRNA data presents an improvement of phylogenetic resolution. We suggest that an integration of explicit clade-specific rRNA structural refinements is not only possible but an important step in the optimization of substitution models dealing with rRNA data.     

Amplified fragment length polymorphisms,the evolution of the land snail genus Theba (Stylommatophora: Helicidae), and an objective approach for relating fossils to internal nodes of a phylogenetic tree using geometric morphometrics

Time‐trees are commonly calibrated based on fossils attributed to internal nodes, thus defining the minimum age of these nodes. However, in the absence of synapomorphies, the phylogenetic position of a fossil can only be inferred based on similarity. In this study, we objectively allocated fossil shells to internal nodes based on the reconstruction of ancestral shapes and sizes in a geometric morphometric framework. Our phylogenetic analysis of 24 (putative sub)species was based on 2524 amplified fragment length polymorphism loci. In this well‐supported tree the taxa occurring in north‐west Africa and on the Iberian peninsula were paraphyletic with respect to the (sub)species from the Canary and Selvagen Islands, indicating a continental origin of the genus in contrast to our earlier sequence‐based account. Ancestral shell shapes and sizes were inferred based on landmark data using squared‐change parsimony. In a subsequent principal component analysis, only three of 20 fossil shells could be unequivocally allocated to internal nodes. However, these fossils were all Quaternary, and thus too young to infer meaningfully narrow confidence intervals for divergence estimates that probably reach back into the Miocene or even Oligocene. The apparent failure of allocating older fossils to internal nodes and achieving a reliable tree calibration was caused by the absence of phylogenetic signal in the shells of Theba due to extensive, sometimes rapid, convergent evolution, including reversals. © 2014 The Linnean Society of London     

AliGROOVE – visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support

Background

Masking of multiple sequence alignment blocks has become a powerful method to enhance the tree-likeness of the underlying data. However, existing masking approaches are insensitive to heterogeneous sequence divergence which can mislead tree reconstructions. We present AliGROOVE, a new method based on a sliding window and a Monte Carlo resampling approach, that visualizes heterogeneous sequence divergence or alignment ambiguity related to single taxa or subsets of taxa within a multiple sequence alignment and tags suspicious branches on a given tree.

Results

We used simulated multiple sequence alignments to show that the extent of alignment ambiguity in pairwise sequence comparison is correlated with the frequency of misplaced taxa in tree reconstructions. The approach implemented in AliGROOVE allows to detect nodes within a tree that are supported despite the absence of phylogenetic signal in the underlying multiple sequence alignment. We show that AliGROOVE equally well detects heterogeneous sequence divergence in a case study based on an empirical data set of mitochondrial DNA sequences of chelicerates.

Conclusions

The AliGROOVE approach has the potential to identify single taxa or subsets of taxa which show predominantly randomized sequence similarity in comparison with other taxa in a multiple sequence alignment. It further allows to evaluate the reliability of node support in a novel way.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-294) contains supplementary material, which is available to authorized users.     

Diversity of Anisoptera (Odonata): infering speciation processes from patterns of morphological diversity

With roughly 2500 described species Anisoptera are among the species-poor suborders within insects. However, morphological and ecological variability are truly impressive. Anisoptera are classified into about 15 families of variable species richness. In this analysis phylogenetic research is integrated with comparative approaches to investigate possible explanations of differential speciation rates within this suborder. A short review of phylogenetic work based on morphological characters is compared to published molecular phylogenies. Sistergroup comparisons are used to elucidate whether a) sexual selection, b) duration of life cycles, or c) differentiation in body size, have had a detectable effect on speciation rate. In all three analyses effects of distributional range and latitudinal distribution were controlled. These analyses suggest sexual selection promotes speciation and an increase in body size is positively correlated with speciation rate. The evolutionary significance of these results is discussed and experimental approaches that should advance our understanding of anisopteran diversity are suggested.