Until recently, phylogenetic analyses of Archaea have mainly been based on ribosomal RNA (rRNA) sequence comparisons, leading to the distinction of the two major archaeal phyla: the Euryarchaeota and the Crenarchaeota. Here, thanks to the recent sequencing of several archaeal genomes, we have constructed a phylogeny based on the fusion of the sequences of the 53 ribosomal proteins present in mo...

Eukaryotic organelles depend on nuclear genes to perpetuate their biochemical integrity. This is true for mitochondria in all eukaryotes and plastids in plants and algae. Then how do kleptoplasts, plastids that are sequestered by some sacoglossan sea slugs, survive in the animals' digestive gland cells in the absence of the algal nucleus encoding the vast majority of organellar proteins? For al...

In Leung et al. (2017), we provide evidence that Drosophila transposons have been major contributors to the expansion of the Drosophila ananassae fourth chromosome (Muller F element) arms. Dunning Hotopp and Klasson agree with this finding, but they take exception to our second conclusion, that lateral gene transfer (LGT) from theWolbachia endosymbiont of D. ananassae (wAna) had only a minor ro...

Over the last 10 years, DNA sequences of more than 600 bacterial species have been deposited in databases and are now available to search any gene, motif, or regulatory sequence of interest. Although genome data are instrumental in phylogenetic analysis and in silico design of metabolic and regulatory networks, only a very small fraction of the information has been experimentally validated. A s...

We extend the inequality of Tomboulis and Yaffe in SU(2) lattice gauge theory (LGT) to SU(N) LGT and to general classical spin systems, by use of reflection positivity. Basically the inequalities guarantee that a system in a box that is sufficiently insensitive to boundary conditions has a non-zero mass gap. We explicitly illustrate the theorem in some solvable models. Strong coupling expansion...

Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these studies is that lateral gene transfer (LGT) has blurred prokaryotic phylogenies to such a degree that the darwinian scheme of treelike evolution might be abandoned in favor of a net or web. Here, we focus...

In a 2+1-dimensional pure LGT at finite temperature the critical coupling for the deconfinement transition scales as βc(nt) = Jcnt + a1, where nt is the number of links in the “time-like” direction of the symmetric lattice. We study the effective action for the Polyakov loop obtained by neglecting the space-like plaquettes, and we are able to compute analytically in this context the coefficient...

Lateral gene transfer (LGT) from prokaryotes to microbial eukaryotes is usually detected by chance through genome-sequencing projects. Here, we explore a different, hypothesis-driven approach. We show that the fitness advantage associated with the transferred gene, typically invoked only in retrospect, can be used to design a functional screen capable of identifying postulated LGT cases. We hyp...

Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Many supertree approaches use optimality criteria that do not reflect underlying pro...