Figure 1 - uploaded by Olaf R P Bininda-Emonds
Content may be subject to copyright.
Representative species of Hymenoptera. The pictured hymenopteran species clockwise from top left are the German wasp (Vespula germanica), red bull ant (Myrmecia gulosa), Argid sawfly (Arge humeralis) and European honey bee (Apis mellifera) (images courtesy of Richard Bartz, user Quartl, Bruce Marlin and Jon Sullivan, respectively; all were obtained from Wikimedia Commons under the Creative Commons Attribution/Share-Alike License except the honey bee, which has been released into the public domain).
Source publication
The combination of molecular sequence data and bioinformatics has revolutionized phylogenetic inference over the past decade, vastly increasing the scope of the evolutionary trees that we are able to infer. A recent paper in BMC Biology describing a new phylogenomic pipeline to help automate the inference of evolutionary trees from public sequence...
Similar publications
Distance methods are ubiquitous tools in phylogenetics.Their primary purpose may be to reconstructevolutionary history, but they are also used as components in bioinformatic pipelines. However, poorcomputational efficiency has been a constraint on the applicability of distance methods on very largeproblem instances.
We present fastphylo, a software...
Citations
... Most phylogenomic analyses start with the identification of ortholog sequences, after some process of sequence collection and pruning of paralogs (e.g., Koonin and Wolf 2008;Dunn et al. 2008;Medina et al. 2011;Sanderson et al. 2011;Bininda-Emonds 2011;Williams et al. 2012;Lang et al. 2013;Romiguier et al. 2013;Salichos and Rokas 2013). Much less often, alternative species tree analyses focus on gene duplication and loss (Katz et al. 2012), or consider paralogs at all (Holton and Pisani 2010). ...
Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting or horizontal gene transfer. In this manuscript we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and incomplete lineage sorting, therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations in order to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models.
... These data can derive either from de novo sequences generated by the researcher and/or from online resources such as GenBank. Indeed, in the latter case, numerous phylogenetic pipelines now exist (see Bininda-Emonds 2011) for the express purpose of mining GenBank and other similar resources for homologous sequence data. However, gene trees represent only one source of data potentially available under a supertree framework. ...
The dominant approach to the analysis of phylogenomic data is the concatenation of the individual gene data sets into a giant supermatrix that is analyzed en masse. Nevertheless, there remain compelling arguments for a partitioned approach in which individual partitions (usually genes) are instead analyzed separately and the resulting trees are combined to yield the final phylogeny. For instance, it has been argued that this supertree framework, which remains controversial, can better account for natural evolutionary processes like horizontal gene transfer and incomplete lineage sorting that can cause the gene trees, although accurate for the evolutionary history of the genes, to differ from the species tree. In this chapter, I review the different methods of supertree construction (broadly defined), including newer model-based methods based on a multispecies coalescent model. In so doing, I elaborate on some of their strengths and weaknesses relative to one another as well as provide a rough guide to performing a supertree analysis before addressing criticisms of the supertree approach in general. In the end, however, rather than dogmatically advocating supertree construction and partitioned analyses in general, I instead argue that a combined, “global congruence” approach in which data sets are analyzed under both a supermatrix (unpartitioned) and supertree (partitioned) framework represents the best strategy in our attempts to uncover the Tree of Life.
... Given the strong differences in opinion expressed by the above authors regarding the use of parametric methods to analyze sparse supermatrices as well as the suitability of lazy, local subtreepruning-regrafting searches in RAxML to conduct those analyses, it is unclear whether the resulting trees should be embraced as ''. . . presenting the state-of-the-art with respect to hypotheses of evolutionary relationships within the group'' (Bininda-Emonds, 2011, p. 1; in reference to Peters et al. (2011)) wherein the bootstrap values are conservative estimates of branch support () or rather an example from bioinformatics wherein, ''Overzealous data mining is seen to have replaced carefully performed experimental analyses. . .'' ...
Macrophages are central elements of all organs, where they have a multitude of physiological and pathological functions. The first macrophages are produced during fetal development, and most adult organs retain populations of fetal-derived macrophages that self-maintain without major input of hematopoietic stem cell-derived monocytes. Their developmental origins make macrophages highly susceptible to environmental perturbations experienced in early life, in particular the fetal period. It is now well recognized that such adverse developmental conditions contribute to a wide range of diseases later in life. This chapter explores the notion that macrophages are key targets of environmental adversities during development, and mediators of their long-term impact on health and disease. We first briefly summarize our current understanding of macrophage ontogeny and their biology in tissues and consider potential mechanisms by which environmental stressors may mediate fetal programming. We then review evidence for programming of macrophages by adversities ranging from maternal immune activation and diet to environmental pollutants and toxins, which have disease relevance for different organ systems. Throughout this chapter, we contemplate appropriate experimental strategies to study macrophage programming. We conclude by discussing how our current knowledge of macrophage programming could be conceptualized, and finally highlight open questions in the field and approaches to address them.
