Resolving Animal Phylogeny: A Sledgehammer for a Tough Nut?

When integration fails: Prokaryote phylogeny and the tree of life

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today's literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history (often called 'universal phylogeny'). Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a 'meta-heuristic' in the normative commitments guiding scientific practice.

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics

Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.

The primary role of fibrinogen-related proteins in invertebrates is defense, not coagulation

In vertebrates, the conversion of fibrinogen into fibrin is an essential process that underlies the establishment of the supporting protein framework required for coagulation. In invertebrates, fibrinogen-domain-containing proteins play a role in the defense response generated against pathogens; however, they do not function in coagulation, suggesting that this role has been recently acquired. Molecules containing fibrinogen motifs have been identified in numerous invertebrate organisms, and most of these molecules known to date have been linked to defense. Moreover, recent genome projects of invertebrate animals have revealed surprisingly high numbers of fibrinogen-like loci in their genomes, suggesting important and perhaps diverse functions of fibrinogen-like proteins in invertebrates. The ancestral role of molecules containing fibrinogen-related domains (FReDs) with immunity is the focus of this review, with emphasis on specific FReDs called fibrinogen-related proteins (FREPs) identified from the schistosome-transmitting mollusc Biomphalaria glabrata. Herein, we outline the range of invertebrate organisms FREPs can be found in, and detail the roles these molecules play in defense and protection against infection.

A twist in time--the evolution of spiral cleavage in the light of animal phylogeny

Recent progress in reconstructing animal relationships enables us to draw a better picture of the evolution of important characters such as organ systems and developmental processes. By mapping these characters onto the phylogenetic framework, we can detect changes that have occurred in them during evolution. The spiral mode of development is a complex of characters that is present in many lineages, such as nemerteans, annelids, mollusks, and polyclad platyhelminthes. However, some of these lineages show variations of this general program in which sub-characters are modified without changing the overlying pattern. Recent molecular phylogenies suggest that spiral cleavage was lost, or at least has deviated from its original pattern, in more lineages than was previously thought (e.g., in rotifers, gastrotrichs, bryozoans, brachiopods, and phoronids). Here, I summarize recent progress in reconstructing the spiralian tree of life and discuss its significance for our understanding of the spiral-cleavage character complex. I conclude that more detailed knowledge of the development of spiralian taxa is necessary to understand the mechanisms behind these changes, and to understand the evolutionary changes and adaptations of spiralian embryos.

An application of supertree methods to Mammalian mitogenomic sequences

TWO DIFFERENT APPROACHES CAN BE USED IN PHYLOGENOMICS: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid missing data, since datasets that are analyzed separately do not need to represent identical taxa. However, the supertree approach and the corresponding consensus methods have been highly criticized for not providing valid phylogenetic hypotheses. In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing 93 mammal families. The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings. The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees. The most similar supertree method was the least congruent with the model trees. We conclude that some of the methods tested are worth considering in a phylogenomic context.

Origin and evolution of chromosomal sperm proteins

In the eukaryotic cell, DNA compaction is achieved through its interaction with histones, constituting a nucleoprotein complex called chromatin. During metazoan evolution, the different structural and functional constraints imposed on the somatic and germinal cell lines led to a unique process of specialization of the sperm nuclear basic proteins (SNBPs) associated with chromatin in male germ cells. SNBPs encompass a heterogeneous group of proteins which, since their discovery in the nineteenth century, have been studied extensively in different organisms. However, the origin and controversial mechanisms driving the evolution of this group of proteins has only recently started to be understood. Here, we analyze in detail the histone hypothesis for the vertical parallel evolution of SNBPs, involving a "vertical" transition from a histone to a protamine-like and finally protamine types (H --> PL --> P), the last one of which is present in the sperm of organisms at the uppermost tips of the phylogenetic tree. In particular, the common ancestry shared by the protamine-like (PL)- and protamine (P)-types with histone H1 is discussed within the context of the diverse structural and functional constraints acting upon these proteins during bilaterian evolution.