Influence of semi-arid environment on radiation use efficiency and other growth attributes of lentil crop.

Solar radiation (SR) is essential for yield improvement in lentil, which is a crop of marginal environments. Herein, experiments were conducted over 2 years under a semi-arid environment to study the radiation interception (RI), efficiency, growth, and development of three lentil genotypes (Punjab Masoor-2009 (PM-2009), NIAB Masoor-2006 (NM-2006), and NIAB Masoor-2002 (NM-2002)) in relation to three nitrogen rates (13, 19, and 25 kg ha-1). Seasonal dynamics of intercepted photoactive radiation (IPAR) and cumulated photosynthetic photon flux density were highly associated with seasonal dynamics of leaf area index (LAI), with a high value of R2 (0.93 and 0.89) across all nitrogen rates and genotypes in both years. Nitrogen application promoted growth, and maximum LAI (3.97 and 3.57) and RI (324 and 301 MJ m-2) were attained for the first and second years of study, respectively. Biomass and yield were positively associated with IPAR. Variation in radiation absorption (RA) among genotypes was due to different patterns of LAI development. In both years, yield (23% and 25%) and radiation use efficiency (RUE) for grain yield (0.44 and 0.37 g MJ-1) were respectively higher for PM-2009 than for the other genotypes. Genotype PM-2009 had 15 days shorter crop cycle than others while 14% higher GDDs accumulated in the first year compared with the second due to the higher temperature. High nitrogen (25 kg ha-1) application resulted in higher dry matter (DM), and grain yield (GY), while RUE and PAR were not statistically different under 19 kg N ha-1 application across years. Genotypes PM-2009 and NM-2006 may perform reasonably well under arid to semi-arid regions at farmer field. These findings may assist researchers and crop modelers to optimize the lentil ideotype for efficient light utilization.

Probabilistic inference of lateral gene transfer events.

BACKGROUND: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge. RESULTS: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify "highways" of LGT. CONCLUSIONS: Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.

Fastphylo: fast tools for phylogenetics.

BACKGROUND: Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances. RESULTS: We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency. CONCLUSIONS: Fastphylo is a fast, memory efficient, and easy to use software suite. Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.