A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data

Phylogeny reconstruction is a difficult computational problem, because the number of possible solutions increases with the number of included taxa. For example, for only 14 taxa, there are more than seven trillion possible unrooted phylogenetic trees. For this reason, phylogenetic inference methods commonly use clustering algorithms (e.g., the neighbor-joining method) or heuristic search strategies to minimize the amount of time spent evaluating nonoptimal trees. Even heuristic searches can be painfully slow, especially when computationally intensive optimality criteria such as maximum likelihood are used. I describe here a different approach to heuristic searching (using a genetic algorithm) that can tremendously reduce the time required for maximum-likelihood phylogenetic inference, especially for data sets involving large numbers of taxa. Genetic algorithms are simulations of natural selection in which individuals are encoded solutions to the problem of interest. Here, labeled phylogenetic trees are the individuals, and differential reproduction is effected by allowing the number of offspring produced by each individual to be proportional to that individual's rank likelihood score. Natural selection increases the average likelihood in the evolving population of phylogenetic trees, and the genetic algorithm is allowed to proceed until the likelihood of the best individual ceases to improve over time. An example is presented involving rbcL sequence data for 55 taxa of green plants. The genetic algorithm described here required only 6% of the computational effort required by a conventional heuristic search using tree bisection/reconnection (TBR) branch swapping to obtain the same maximum-likelihood topology.      

Effect of harvesting on temporal papyrus (<Emphasis Type="Italic">Cyperus papyrus</Emphasis>) biomass regeneration potential among swamps in Winam Gulf wetlands of Lake Victoria Basin,Kenya

This study established for the first time the impact of harvesting on post-harvest papyrus (Cyperus papyrus L.) biomass regeneration potential, with two harvesting regimes compared. Above-ground papyrus biomass was determined. Biomass varied with site. Site had no effect on regeneration potential, but monthly harvesting reduced papyrus biomass regeneration potential among sites. However, seasonal (6-monthly) harvesting did not appear to affect papyrus biomass regeneration potential. Exponential and polynomial trend analyses revealed a consistent downward trend for monthly harvest biomass, and the polynomial trend was more linear (F = 97.913; P < 0.001) than periodic (F = 9.617; P < 0.05). The polynomial trend scenario indicated how papyrus biological dynamics are likely to behave as monthly harvests are repeated. This suggests that regeneration potential is significantly reduced with successive monthly harvest, leading to weak spatial connectivity, papyrus stand fragmentation, and increased landscape patchiness. A 6-month harvest regime can be established to regenerate more biomass between harvests than is currently the case, with positive implications for wetland conservation and carbon sequestration. Papyrus harvesters can be kept off the swamps by establishing a riparian buffer zone of agro forestry trees and shrubs which can substitute for the papyrus as it is left to mature. However, while the information presented is useful for papyrus wetland management strategies, it is recognized that the study period was too short to permit a generalized recommendation.     

The Mouse Limb Anatomy Atlas: An interactive 3D tool for studying embryonic limb patterning

Background  

The developing mouse limb is widely used as a model system for studying tissue patterning. Despite this, few references are available that can be used for the correct identification of developing limb structures, such as muscles and tendons. Existing textual references consist of two-dimensional (2D) illustrations of the adult rat or mouse limb that can be difficult to apply when attempting to describe the complex three-dimensional (3D) relationship between tissues.     

Improving the performance of the EPT Index to accommodate multiple stressors in Afrotropical streams

The EPT index (Ephemeroptera, Plecoptera and Trichoptera) may be skewed by the wide tolerance to multiple stressors of the Baetid, Caenid and Hydropsychid families, which affects the performance of the EPT index as an indicator of multiple stressors in aquatic ecosystems. The effect of the BCH families on the EPT index was evaluated and alternatives were considered to improve its performance. The hypothesis that the removal of the BCH families improves sensitivity of the EPT index to human-induced stressors in streams and rivers was tested. Macroinvertebrates were collected in January–March 2009 at 22 sites in the Nyando and Nzoia Rivers, Lake Victoria basin, Kenya. Nine derivatives and modifications of the EPT index were tested for responses to a disturbance gradient, ranked into three condition categories (reference, intermediate and impaired). The sensitivity of the proportionate abundance derivative of the EPT index improved when the BCH families were removed, whereas that of the richness derivative improved marginally. Other modifications considered performed poorly when compared with the EPT-BCH metrics. Wide distribution of the BCH across all sites, irrespective of the level of disturbance, reduced the sensitivity of the EPT index in the studied streams. The removal of the BCH families enhanced the sensitivity of the index to multiple stressors in Afrotropical streams and rivers.