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New and Exciting in PLoS ONE

There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Leptin Affects Life History Decisions in a Passerine Bird: A Field Experiment:

Organisms face trade-offs regarding their life-history strategies, such as decisions of single or multiple broods within a year. In passerines displaying facultative multiple breeding, the probability of laying a second clutch is influenced by several life-history factors. However, information about the mechanistic background of these trade-offs is largely lacking. Leptin is a protein hormone produced by white fat cells, and acts as a signal between peripheral energy depots and the central nervous system. In addition, leptin affects cells at all levels of the reproductive axis and plays a critical role in regulating the allocation of metabolic energy to reproduction. As such, it is possible that leptin levels influence the decision of whether or not to invest time and energy into a second clutch. Accordingly, we expect a treatment with exogenous leptin to result in an increased number of second broods. At a later stage during the first brood, female great tits were treated either with long-term leptin-filled cholesterol pellets (the experimental birds) or with pellets containing only cholesterol (the control birds). We found that leptin-treated females were significantly more likely to have a second brood and that the earlier females were more likely to lay a second clutch than the late females. As both timing of first brood and treatment with leptin were important in the decision of having multiple broods, the trade-offs involved in the breeding strategy most likely depend on multiple factors. Presumably leptin has evolved as a signal of energy supply status to regulate the release of reproductive hormones so that reproduction is coordinated with periods of sufficient nutrients. This study investigated the role of leptin as a mediator between energy resources and reproductive output, providing a fundamentally new insight into how trade-offs work on a functional basis.

Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws:

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny? In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods. All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors -uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees. There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees.