Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway.

Background and Aims: Investigating species distributions across geographic barriers is a commonly utilized method in biogeography to help understand the functional traits that allow plants to disperse successfully. Here the biogeographic pattern analysis approach is extended by using chloroplast DNA whole-genome 'mining' to examine the functional traits that have impacted the dispersal of widespread temperate forest species across an intermittent seaway, the 200 km wide Bass Strait of south-eastern Australia. Methods: Multiple, co-distributed species of both dry and wet forests were sampled from five regions on either side of the Strait to obtain insights into past dispersal of these biomes via seed. Using a next-generation sequencing-based pool-seq method, the sharing of single nucleotide polymorphisms (SNPs) was estimated between all five regions in the chloroplast genome. Key Results: A total of 3335 SNPs were detected in 20 species. SNP sharing patterns between regions provided evidence for significant seed-mediated gene flow across the study area, including across Bass Strait. A higher proportion of shared SNPs in dry forest species, especially those dispersed by birds, compared with wet forest species suggests that dry forest species have undergone greater seed-mediated gene flow across the study region during past climatic oscillations and sea level changes associated with the interglacial/glacial cycles. Conclusions: This finding is consistent with a greater propensity for long-distance dispersal for species of open habitats and proxy evidence that expansive areas of dry vegetation occurred during times of exposure of Bass Strait during glacials. Overall, this study provides novel genetic evidence that habitat type and its interaction with dispersal traits are major influences on dispersal of plants.

Quantification of historical livestock importation into New Zealand 1860-1979.

AIMS: To quantify the numbers of live cattle, sheep and poultry imported into New Zealand and, where possible, their country of origin from 1860 to 1979. METHODS: Information on the origin and number of live animal importations into New Zealand was collected for cattle, sheep and poultry for the period 1868-1979 from the annual reports compiled by the New Zealand Registrar General's Office, Government Statistician's Office, Census and Statistics Office, Census and Statistics Department, Customs Department and Department of Statistics. Census data from 1851 to 1871 were also used to estimate the livestock population during this period. The number of animals imported and the mean population for each species in a decade were determined, and the major countries of origin were identified. RESULTS: A large number of cattle (53,384) and sheep (604,525) were imported in the 1860s, and then there was a marked reduction in importations. Live poultry were imported in relatively small numbers (20,701) from 1880 to 1939, then 1,564,330 live poultry were imported between 1960 and 1979. Australia was the predominant country of origin for sheep between 1868 and 1959 (51,347/60,918; 84.3%) and of cattle between 1868 and 1979 (10,080/15,157; 66.5%). Only 6,712 (11.0%) sheep and 3,909 (25.8%) cattle were imported from the United Kingdom over the same periods, and even fewer from other countries. CONCLUSIONS: The collated data and historical reports show that from 1860 to 1979 Australia has been the main source of livestock introduced into New Zealand. The pattern of importation showed that large numbers of cattle and sheep were initially imported in the 1860s, probably in response to rapid agricultural expansion. Thereafter importations continued at much reduced numbers. In contrast, relatively small numbers of poultry were introduced until the 1960s when large numbers were imported as part of the development of a modern high-production industry. The overall pattern for both cattle and sheep was of a bottleneck event, as initially a relatively limited number of animals arrived from outside populations, followed by population expansion with ongoing but limited immigration (admixture). Investigation into the genetic population structure of New Zealand's cattle and sheep, as well as their host-associated microorganisms, could reflect the impact of these early historical events.

The algebra of the general Markov model on phylogenetic trees and networks.

It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the associated Hadamard transformation, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper, we rectify this shortcoming by showing how to extend the general Markov model on trees to include incompatible edges; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the "splitting" operator that generates the branching process on phylogenetic trees. For simplicity, we proceed by discussing the two state case and then show that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the Hadamard approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give an argument that our extension to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications.

Treeness triangles: visualizing the loss of phylogenetic signal.

It is well known that molecular data "saturates" with increasing sequence divergence (thereby losing phylogenetic information) and that in addition the accumulation of misleading information due to chance similarities or to systematic bias may accompany saturation as well. Exploratory data analysis methods that can quantify the extent of signal loss or convergence for a given data set are scarce. Such methods are needed because genomics delivers very long sequence alignments spanning substantial phylogenetic depth, where site saturation may be compounded by systematic biases or other alternative signals. Here we introduce the Treeness Triangle (TT) graph, in which signals detectable by Hadamard (spectral) analysis are summed into 3 categories--those supporting 1) external and 2) internal branches in the optimal tree, in addition to 3) the residuals (potential internal branches not present in the optimal tree). These 3 values are plotted in a standard ternary coordinate system. The approach is illustrated with simulated and real data sets, the latter from complete chloroplast genomes, where potential problems of paralogy or lateral gene acquisition can be excluded. The TT uncovers the divergence-dependent loss of phylogenetic signal as subsets of chloroplast genomes are investigated that span increasingly deeper evolutionary timescales. The rate of signal loss (or signal retention) varies with the gene and/or the method of analysis.

Selecting representative model micro-organisms.

BACKGROUND: Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species. RESULTS: We develop the Best Total Coverage (BTC) method for selecting one or more representative model organisms from a group of interest, given that rough genetic distances between the members of the group are known. Software implementing a "greedy" version of the method can be used with large data sets, its effectiveness is tested using both constructed and biological data sets. CONCLUSION: In both the simulated and biological examples the greedy-BTC method outperformed random selection of model organisms, and for two biological examples it outperformed selection of model strains based on phylogenetic structure. Although the method was designed with microbial species in mind, and is tested here on three microbial data sets, it will also be applicable to other types of organism.

The MinMax Squeeze: guaranteeing a minimal tree for population data.

We report that for population data, where sequences are very similar to one another, it is often possible to use a two-pronged (MinMax Squeeze) approach to prove that a tree is the shortest possible under the parsimony criterion. Such population data can be in a range where parsimony is a maximum likelihood estimator. This is in sharp contrast to the case with species data, where sequences are much further apart and the problem of guaranteeing an optimal phylogenetic tree is known to be computationally prohibitive for realistic numbers of species, irrespective of whether likelihood or parsimony is the optimality criterion. The Squeeze uses both an upper bound (the length of the shortest tree known) and a lower bound derived from partitions of the columns (the length of the shortest tree possible). If the two bounds meet, the shortest known tree is thus proven to be a shortest possible tree. The implementation is first tested on simulated data sets and then applied to 53 complete human mitochondrial genomes. The shortest possible trees for those data have several significant improvements from the published tree. Namely, a pair of Australian lineages comes deeper in the tree (in agreement with archaeological data), and the non-African part of the tree shows greater agreement with the geographical distribution of lineages.

Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study.

We conducted a simulation study of the phylogenetic methods UPGMA, neighbor joining, maximum parsimony, and maximum likelihood for a five-taxon tree under a molecular clock. The parameter space included a small region where maximum parsimony is inconsistent, so we tested inconsistency correction for parsimony and distance correction for neighbor joining. As expected, corrected parsimony was consistent. For these data, maximum likelihood with the clock assumption outperformed each of the other methods tested. The distance-based methods performed marginally better than did maximum parsimony and maximum likelihood without the clock assumption. Data correction was generally detrimental to accuracy, especially for short sequence lengths. We identified another region of the parameter space where, although consistent for a given method, some incorrect trees were each selected with up to twice the frequency of the correct (generating) tree for sequences of bounded length. These incorrect trees are those where the outgroup has been incorrectly placed. In addition to this problem, the placement of the outgroup sequence can have a confounding effect on the ingroup tree, whereby the ingroup is correct when using the ingroup sequences alone, but with the inclusion of the outgroup the ingroup tree becomes incorrect.

Delta plots: a tool for analyzing phylogenetic distance data.

A method is described that allows the assessment of treelikeness of phylogenetic distance data before tree estimation. This method is related to statistical geometry as introduced by Eigen, Winkler-Oswatitsch, and Dress (1988 [Proc. Natl. Acad. Sci. USA. 85:5913-5917]), and in essence, displays a measure for treelikeness of quartets in terms of a histogram that we call a delta plot. This allows identification of nontreelike data and analysis of noisy data sets arising from processes such as, for example, parallel evolution, recombination, or lateral gene transfer. In addition to an overall assessment of treelikeness, individual taxa can be ranked by reference to the treelikeness of the quartets to which they belong. Removal of taxa on the basis of this ranking results in an increase in accuracy of tree estimation. Recombinant data sets are simulated, and the method is shown to be capable of identifying single recombinant taxa on the basis of distance information alone, provided the parents of the recombinant sequence are sufficiently divergent and the mixture of tree histories is not strongly skewed toward a single tree. delta Plots and taxon rankings are applied to three biological data sets using distances derived from sequence alignment, gene order, and fragment length polymorphism.

Multiple maxima of likelihood in phylogenetic trees: an analytic approach.

Maximum likelihood (ML) is a widely used criterion for selecting optimal evolutionary trees. However, the nature of the likelihood surface for trees is still not sufficiently understood, especially with regard to the frequency of multiple optima. Here, we initiate an analytic study for identifying sequences that generate multiple optima. We concentrate on the problem of optimizing edge weights for a given tree or trees (as opposed to searching through the space of all trees). We report a new approach to computing ML directly, which we have used to find large families of sequences that have multiple optima, including sequences with a continuum of optimal points. Such data sets are best supported by different (two or more) phylogenies that vary significantly in their timings of evolutionary events. Some standard biological processes can lead to data with multiple optima, and consequently the field needs further investigation. Our results imply that hill-climbing techniques as currently implemented in various software packages cannot guarantee that one will find the global ML point, even if it is unique.

[Comparison of ventilation-/perfusion scintigraphy with spiral CT in acute lung embolism]. / Vergleich der Ventilations-/Perfusions-Szintigraphie mit der Spiral-CT bei akuter Lungenembolie.

AIM: Evaluation of the validity of spiral-CT compared with ventilation/perfusion (v/p) scintigraphy, the standard diagnostic tool in patients with suspected pulmonary embolism. PATIENTS AND METHODS: Prospective study of 70 patients with symptoms of acute pulmonary embolism: examination with both methods within 4 hours. RESULTS: In 46 patients pulmonary embolism could be unequivocally excluded by both methods. Patients with high-probability-Tc-scans predominantly had central emboli on CT. In cases with medium or low probability-Tc-scans thrombi were usually visible in segmental arteries. In one patient with a non-suspicious scintigram spiral-CT was able to detect emboli in multiple segmental arteries. CONCLUSION: Spiral-CT is a fast, safe and almost always available method for detection of pulmonary embolism. In our hands it is superior to v/p-scintigraphy. It allows direct detection of a thrombus and has additional advantages in differential diagnosis (e. g. lung carcinoma, infectious infiltration). In patients with clinical suspicion of pulmonary embolism spiral-CT should be the primary diagnostic modality.

[Calcifying tendinitis of the femur--diagnosis and differential diagnosis exemplified by 5 cases]. / Die kalzifizierende Tendinitis am Femur--Diagnose und Differentialdiagnose am Beispiel von 5 Fällen.

Five cases of calcifying tendinitis of the femur are presented. Diagnosis were proved histologically or catamnestically. The calcifying tendinitis occurred secondary to localized regressive changes in 3 patients; in 2 cases systemic inflammatory disease had to be assumed. In patients with unclear femoral pain and radiologically visible calcifications, especially at the linea aspera, one should include a calcifying tendinitis in the differential diagnosis besides juxtacortical osteosarcoma and myositis ossificans. This entity can sometimes be a symptom of systemic disease such as psoriasis and palmoplantar pustulosis.

[Spiral computerized tomography of acute abdominal aortic aneurysm with optimal 3-D image reconstruction]. / Spiral-Computertomographie des akuten Bauchaortenaneurysmas mit optionaler 3-D-Bildrekonstruktion.

43 of 46 consecutive patients with suspected rupture of abdominal aortic aneurysm could be examined by spiral CT. Rupture of an abdominal vessel was found in 18 patients and proved by surgery. Size and extent of the aneurysm, rupture, dissection and vascular occlusion were demonstrated quickly and precisely by spiral CT, planning of surgical intervention could be optimized. Using spiral CT unnecessary explorative laparotomies could be avoided in 25 patients. In addition spiral CT offers the possibility of multiplanar reconstruction images with spatial visualisation of the vascular system. In 8 patients DSA offered no advantage in comparison with 3-D reconstruction images. Spiral CT meets all requirements for quick and reliable diagnosis in suspected rupture of abdominal vessels. Other imaging modalities like digital subtraction angiography are not necessary for evaluation of abdominal aortic aneurysms.

[Experimental studies of the visualization of the vertebral body spongiosa by high-resolution computed tomography]. / Experimentelle Untersuchungen zur Darstellbarkeit von Wirbelkörperspongiosa in der hochauflösenden Computertomographie.

AIM: To show the accuracy and the lower limit of visualisation of cancellous bone in high-resolution computed tomography (HR-CT). METHODS: 18 native human lumbar vertebrae were placed in a water phantom and examined by HR-CT. The scans were compared with contact radiographs of correlating thin bone sections by morphologic criteria. RESULTS AND CONCLUSION: The measured lower limit of visualisation of cancellous bone structures is clearly worse than expected from the measurements of spatial resolution with standard phantoms used for HR-CT (0.6 versus 0.4 mm). True and exact imaging of normal cancellous bone cannot be achieved even by modern HR-CT. Noise creates structures mimicking cancellous bone.

[MRI diagnosis of bone tumors]. / MR-Diagnostik von Knochentumoren.

Diagnosis of bone tumours is still based on plain films and, if necessary, computed tomography because crucial morphologic criteria such as ossification of tumour matrix, patterns of bone destruction and formation of new bone are not clearly visualized by MRI. Only in a few cases is MRI helpful for characterization of bone lesions. Although MRI is of limited value for differential diagnosis of bone tumours, it may be very helpful for planning of biopsy or surgery by virtue of its ability to demonstrate tumour extent and soft tissue changes. For local staging and follow-up of primary bone tumours MRI is clearly the method of choice. MRI strategy should be coordinated with clinical requirements in order to ensure optimum evaluation of tumour extent, effectiveness of chemotherapy and detection of local recurrence.

Rare case of a primary malignant fibrous histiocytoma of the brain.

A rare case of primary MFH of the brain is described together with the CT and MRI findings. The radiological appearance of this tumor is discussed in conjunction with the material published in other case reports.

[Magnetic resonance tomographic results in bone changes associated with sclerosis]. / Kernspintomographische Ergebnisse bei Knochenveränderungen mit Sklerose.

We have compared the value of MRI with conventional radiography and CT in 40 predominantly sclerotic skeletal lesions. We have found that sclerosis and other changes in the bone structure can be demonstrated by MRI in much the same way as with conventional radiography and CT. Using high resolution surface coils, it is possible to demonstrate small areas of new bone formation such as periosteal new bone or the calcification within the nidus of an osteoid osteoma. MRI is particularly appropriate if it is necessary to show soft tissue changes within an area of sclerosis, which may be responsible for the new bone formation and which may be masked on radiographs and CT by the surrounding sclerosis.