Detecting the Dependent Evolution of Biosequences

A probabilistic graphical model is developed in order to detect the dependent evolution between different sites in biological sequences. Given a multiple sequence alignment for each molecule of interest and a phylogenetic tree, the model can predict potential interactions within or between nucleic acids and proteins. Initial validation of the model is carried out using tRNA sequence data. The model is able to accurately identify the secondary structure of tRNA as well as several known tertiary interactions

Lichenometric dating (lichenometry) and the biology of the lichen genus rhizocarpon:challenges and future directions

Lichenometric dating (lichenometry) involves the use of lichen measurements to estimate the age of exposure of various substrata. Because of low radial growth rates and considerable longevity, species of the crustose lichen genus Rhizocarpon have been the most useful in lichenometry. The primary assumption of lichenometry is that colonization, growth and mortality of Rhizocarpon are similar on surfaces of known and unknown age so that the largest thalli present on the respective faces are of comparable age. This review describes the current state of knowledge regarding the biology of Rhizocarpon and considers two main questions: (1) to what extent does existing knowledge support this assumption; and (2) what further biological observations would be useful both to test its validity and to improve the accuracy of lichenometric dates? A review of the Rhizocarpon literature identified gaps in knowledge regarding early development, the growth rate/size curve, mortality, regeneration, competitive effects, colonization, and succession on rock surfaces. The data suggest that these processes may not be comparable on different rock surfaces, especially in regions where growth rates and thallus turnover are high. In addition, several variables could differ between rock surfaces and influence maximum thallus size, including rate and timing of colonization, radial growth rates, environmental differences, thallus fusion, allelopathy, thallus mortality, colonization and competition. Comparative measurements of these variables on surfaces of known and unknown age may help to determine whether the basic assumptions of lichenometry are valid. Ultimately, it may be possible to take these differences into account when interpreting estimated dates

A high resolution map of soil types and physical properties for Cyprus : a digital soil mapping optimization

Fine-resolution soil maps constitute important data for many different environmental studies. Digital soil mapping techniques represent a cost-effective method to obtain detailed information about soil types and soil properties over large areas. The main objective of the study was to extend predictions from 1:25,000 legacy soil surveys (including WRB soil groups, soil depth and soil texture classes) to the larger area of Cyprus. A multiple-trees classification technique, namely Random Forest (RF), was applied. Specific objectives were: (i) to analyze the role and importance of a large data set of environmental predictors, (ii) to investigate the effect of the number of training points, forest size (ntree), the numbers of predictors sampled per node (mtry) and tree size (nodesize) in RF; (iii) to compare RF-derived maps with maps derived with a multinomial logistic regression model, in terms of validation error (test set and independent profiles) and map uncertainty, using the confusion index and a newly developed reliability index. The optimized RF model was run using half of the input points available (over a million) and with ntree equal to 350. The mtry parameter was set to 5 (close to half the number of the environmental variables used) for both soil series and soil properties. The nodesize calibration showed no relevant performance increase and was kept at its default value (1). In terms of environmental variables, the model used 10 predictors, covering all the soil formation factors considered in the scorpan formula, to derive the three maps. Soil properties, derived from geochemistry data, showed a high importance in deriving soil groups, depths and texture. Random Forest constructed a better predictive model than multinomial logistic regression, showing comparable predictive uncertainty but much lower validation error. The RF-derived maps show very low out of bag (OOB) errors (around 10% for both soil groups and soil properties) but relatively high validation error from independent profiles (45% for soil depth, 51% for soil texture). The resulting reliability index was low in the main mountainous area of Cyprus, where predictions were extrapolations as indicated by the multivariate environmental similarity surface, but medium to high in the main agricultural areas of the country

Lichenometry on Adelaide Island, Antarctic Peninsula : size-frequency studies, growth rates and snowpatches

This paper presents new lichenometric population data from the Antarctic Peninsula (67°S), and describes a new approach to lichen growth-rate calibration in locations where dated surfaces are extremely rare. We use historical aerial photography and field surveys to identify sites of former perennial snowpatches where lichen populations now exist. As an independent check on lichen mortality by snowkill, and the timing of snow patch disappearance, we use a positive-degree day (PDD) approach based on monthly climate data from Rothera Research Station. We find that maximum growth rates for lichens <40 mm in diameter on Adelaide Island are around 0.8 mm/yr. Furthermore, we propose that our combined methodology may be more widely applicable to the Polar Regions where the construction of lichenometric dating (age-size) curves remains a problem

Lichenometric dating: a commentary, in the light of some recent statistical studies

This commentary article discusses the relative merits of new mathematical approaches to lichenometry. It highlights their strong reliance on complex statistics; their user un-friendliness; and their occasional mistreatment of existing lichenometric techniques. The article proposes that the success of lichenometric dating over the past 50 years has stemmed from its relative simplicity, transparency, and general field applicability. It concludes that any new techniques which ignore these principles are likely to be unjustified, unsuitable to the user community and inappropriate for the subject matter. Furthermore, the article raises a more general philosophical question: can statistical complexity and high precision in a ‘geobotanical’ dating technique, fraught with high degrees of environmental variability and in-built uncertainty, ever be scientifically valid