MOTIVATION Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. RESULTS We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP...

■ Abstract Until recently, studies of plant reproductive systems have been at the population level, using microevolutionary approaches. The development of cladistic approaches, combined with the emergence of molecular systematics, has resulted in an explosion of phylogenetic studies and an increase in interdisciplinary approaches combining ecological and systematic methodology. These new approa...

Although phylogenetic-based approaches have been frequently used to infer ecological processes, they have been increasingly criticized in recent years. To date, the factors that affect phylogenetic signals and further the ability of phylogenetic distance to predict trait dispersion have been assumed but not empirically tested. Therefore, we investigate which factors potentially influence the ab...

28 We examined developmental programming studies that reported sex-specific effects 29 published between 2012 and 2014, and examined whether the authors reported a 30 statistical approach to explicitly test whether the effect of treatment differed between the 31 sexes, e.g., a sex by treatment interaction term. Less than half of the studies that reported 32 sex-specific effects described explic...

The planning of large infrastructure projects such as inner-city subway tracks is a highly collaborative process in which numerous experts from different domains are involved. While performing the planning task, widely differing scales have to be taken into consideration, ranging from the kilometer scale for the general routing of the track down to the centimeter scale for the detailed design o...

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-th...

In this article, we provide an overview of maximum likelihood methods for phylogenetic inference. A brief introduction to general maximum likelihood estimation is provided. We define a phylogenetic likelihood, summarize how to compute this likelihood, and then discuss approaches used to maximize the phylogenetic likelihood function. We discuss a property of the maximum likelihood estimation, ca...

Orthologous sequences of six nuclear genes were obtained for all recognized genera of New World monkeys (Primates: Platyrrhini) and outgroups to evaluate the phylogenetic relationships and to estimate divergence times. Phylogenetic relationships were reconstructed by maximum parsimony, maximum likelihood, and Bayesian approaches. All methods resolved with 100% branch support genus-level relatio...

Theories of plant defense expression are typically based on the concepts of tradeoffs among traits and of phylogenetic conservatism within clades. Here, I review recent developments in phylogenetic approaches to understanding the evolution of plant defense strategies and plant-herbivore coevolutionary interactions. I focus particularly on multivariate defense against insect herbivores, which is...

With the advent of next generation sequencing technologies, alignment and phylogeny estimation of datasets with thousands of sequences is being attempted. To address these challenges, new algorithmic approaches have been developed that have been able to provide substantial improvements over standard methods. This paper focuses on new approaches for ultra-large tree estimation, including methods...