Birding and DNA: species for the new millennium

Capsule Based on the 1999 Witherby Memorial Lecture – reviews how developments in molecular and population genetics have led to a reappraisal of species limits in birds.

The taxonomy of birds of the West Palearctic has moved from the comparative stability of the ‘Voous List’ into a period of serious activity, with new data emerging in almost every issue of every evolutionary and avian journal! This activity comes from two directions. Firstly, developments in population genetics, molecular biology, acoustics, behaviour and distributional studies have opened new avenues to measuring differentiation among groups of birds. This, in turn, has led to the recognition that earlier views of what constitutes a ‘species’ are in need of modification (‘improvement’), and the emergence of the ‘lineage concept’ of species. I review some of the species concepts most relevant to avian studies, and attempt to show how and why this change has happened, and its consequences for taxonomy and species limits. Examples are given in the form of ‘case studies’, and include Carrion/Hooded Crows Corvus corone/cornix, Green-winged/Eurasian Teals Anas carolinensis/crecca and Phylloscopus warblers.     

EGID: an ensemble algorithm for improved genomic island detection in genomic sequences

Genomic islands (GIs) are genomic regions that are originally transferred from other organisms. The detection of genomic islands in genomes can lead to many applications in industrial, medical and environmental contexts. Existing computational tools for GI detection suffer either low recall or low precision, thus leaving the room for improvement. In this paper, we report the development of our Ensemble algorithm for Genomic Island Detection (EGID). EGID utilizes the prediction results of existing computational tools, filters and generates consensus prediction results. Performance comparisons between our ensemble algorithm and existing programs have shown that our ensemble algorithm is better than any other program. EGID was implemented in Java, and was compiled and executed on Linux operating systems. EGID is freely available at http://www5.esu.edu/cpsc/bioinfo/software/EGID.     

Accurate intraocular pressure prediction from applanation response data using genetic algorithm and neural networks

The fact that Goldmann applanation tonometry does not accurately account for individual corneal elastic stiffness often leads to inaccuracy in the measurement of intraocular pressure (IOP). IOP should account not only for the effect of central corneal thickness (CCT) but should also account for other corneal biomechanical factors. A computational method for accurate and reliable determination of IOP is investigated with a modified applanation tonometer in this paper. The proposed method uses a combined genetic algorithm/neural network procedure to match the clinically measured applanation force-displacement history with that obtained from a nonlinear finite element simulation of applanation. An additional advantage of the proposed method is that it also provides the ability to determine CCT and material properties of the cornea from the same applanation response data. The performance of the proposed method has been demonstrated through a parametric study and via comparison with a well known clinical case. The proposed method is also shown to be computationally efficient, which is an important practical consideration for clinical application.     

Regional species richness,hydrological characteristics and the local species richness of assemblages of North American stream fishes

1. Local assemblage structure, from a deterministic perspective, is presumably dictated by the regional species pool as well as regulated by local factors. We examined the relationships of the regional species pool and local hydrological characteristics to local species richness of North American freshwater fishes using data sets collected during the National Water Quality Assessment program conducted by the United States Geological Survey. 2. We predicted that local species richness is ultimately constrained by the composition of the regional species pool and further associated with local hydrological factors. Moreover, we predicted that variation in local species richness within major families can be explained by different combinations of hydrological characteristics that represent lineage‐specific responses to the environment. 3. Daily discharge and regional and local species richness data were assembled from 41 stream localities across the United States. Multiple stepwise regressions were conducted to predict local species richness, based on regional species richness, mean discharge and hydrological characteristics quantified by nine variables characterising flow variability. Species richness at each site was calculated for the entire assemblage as well as within the four most species‐rich families in the data set (Catostomidae, Centrarchidae, Cyprinidae and Percidae). 4. Local species richness was best predicted by a combination of regional species richness and discharge magnitude when all species were considered. Regional species richness was a significant explanatory variable of local species richness for three of four families (Catostomidae, Centrarchidae, Cyprinidae), but not for Percidae. Local richness in Centrarchidae and Cyprinidae was positively correlated with temporal flow variability as well as high and low flow duration, respectively, while richness in Catostomidae and Percidae tended to be associated with discharge volume. In addition, local species richness for three of the four major families was positively correlated with species richness of the other families in the assemblage, potentially suggesting the influence of local habitat quality and heterogeneity. 5. Results suggest the importance of the combined influences of the regional species pool and local hydrological characteristics on local richness in freshwater fishes, with variation in richness within each family predicted by different characteristics of flow regimes.     

Relative longevity and field metabolic rate in birds

Metabolism is a defining feature of all living organisms, with the metabolic process resulting in the production of free radicals that can cause permanent damage to DNA and other molecules. Surprisingly, birds, bats and other organisms with high metabolic rates have some of the slowest rates of senescence begging the question whether species with high metabolic rates also have evolved mechanisms to cope with damage induced by metabolism. To test whether species with the highest metabolic rates also lived the longest I determined the relationship between relative longevity (maximum lifespan), after adjusting for annual adult survival rate, body mass and sampling effort, and mass-specific field metabolic rate (FMR) in 35 species of birds. There was a strongly positive relationship between relative longevity and FMR, consistent with the hypothesis. This conclusion was robust to statistical control for effects of potentially confounding variables such as age at first reproduction, latitude and migration distance, and similarity in phenotype among species because of common phylogenetic descent. Therefore, species of birds with high metabolic rates senesce more slowly than species with low metabolic rates.