Do orthologous gene phylogenies really support tree-thinking?

Abstract

BackgroundSince Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.ResultsHeat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer.ConclusionOur phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

Pattern pluralism and the Tree of Life hypothesis

“…Because there is substantial disagreement among prokaryotic molecular data sets and little strongly supported congruent signal among data sets that do not clearly disagree, a claim that a hierarchical pattern of groups subordinate to groups is the universal natural order cannot be sustained as an explanandum (6,8,18). (That many seemingly different analyses of these data nevertheless do agree in some ways is not surprising and is discussed later.)…”

“…LGT and the Disappearance of the Explanandum Leaving aside the weakness of phylogenetic signal, which plagues most phylogenetic analyses (18,40), molecular data sets substantially disagree at many levels of analysis, particularly because of LGT. Although there is increasing evidence for the importance of LGT in the evolution of eukaryotes, especially unicells (41), again we focus on prokaryotes; because LGT is almost certainly more frequent among them, much more extensive and relevant comparative genomic data are available for them, and two-thirds of the history of life (and thus, of the TOL) is theirs.…”

“…For many of its supporters, the TOL is a biological fact (a reality outside of our own minds), first established nearly 150 years ago by Darwin, and needing only elaboration (16). For those who question it, the TOL is a scientific hypothesis (a heuristic epistemological model), forcefully and eloquently articulated by Darwin but not yet proven to be true (17,18). We develop this second position here, suggesting a formulation of the TOL hypothesis that might generally be accepted as being faithful to Darwin's original intent, and discussing its testability and status in the context of prokaryotic data.…”

Dealing with incongruence in phylogenomic analyses

“…The first one means focusing on conflicts, and denying the building of a species tree as soon as significant disagreement is detected (Bapteste et al 2005;Comas et al 2006;Susko et al 2006). The second view means averaging the phylogenetic signal across genes without considering the variance (basic supertree and supermatrix approaches).…”

Optical, Biochemical, and Molecular Characterization of New Bioluminescence Systems

“…The FMNH 2 is a by-product of the respiratory chain and is therefore continuously available for bioluminescence. Thus, in the bacterial system, the level of luciferase controls the amount of light produced (26,27).…”