The reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences. We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server. The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.

Phylogenetic position of the marine biflagellate Palpitomonas bilix is intriguing, since several ultrastructural characteristics implied its evolutionary connection to Archaeplastida or Hacrobia. The origin and early evolution of these two eukaryotic assemblages have yet to be fully elucidated, and P. bilix may be a key lineage in tracing those groups' early evolution. In the present study, we analyzed a ‘phylogenomic' alignment of 157 genes to clarify the position of P. bilix in eukaryotic phylogeny. In the 157-gene phylogeny, P. bilix was found to be basal to a clade of cryptophytes, goniomonads and kathablepharids, collectively known as Cryptista, which is proposed to be a part of the larger taxonomic assemblage Hacrobia. We here discuss the taxonomic assignment of P. bilix, and character evolution in Cryptista.

The reconstruction of ancestral scenarios is widely used to study the evolution of characters along a phylogenetic tree. In the likelihood framework one commonly uses the marginal posterior probabilities of the character states, and the joint reconstruction of the most likely scenario. Both approaches are somewhat unsatisfactory. Marginal reconstructions provide users with state probabilities, but these are difficult to interpret and visualize, while joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts and the Brier criterion to associate each node in the tree to a set of likely states. A unique state is predicted in the tree regions with low uncertainty, while several states are predicted in the uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated to the same states and use graph visualization tools. The method is implemented in the PastML program and web server.The results on simulated data consistently show the accuracy and robustness of the approach. The method is applied to large tree comprising 3,619 sequences from HIV-1M subtype C sampled worldwide, which is processed in a few minutes. Results are very convincing: we retrieve and visualize the main transmission routes of HIV-1C; we demonstrate that drug resistance mutations mostly emerge independently under treatment pressure, but some resistance clusters are found, corresponding to transmissions among untreated patients.A central issue in biology is to recover and understand the evolutionary history of biological entities. These may be of different nature and scale, ranging from DNA and proteins to communities, going through biological systems, organs, strains, individuals, species and populations. The characteristics and evolution of these objects are measured using a variety of

Organisms with nonphotosynthetic plastids often retain genomes; their gene contents provide clues as to the functions of these organelles. Yet the functional roles of some retained genes-such as those coding for ATP synthase-remain mysterious. In this study, we report the complete plastid genome and transcriptome data of a nonphotosynthetic diatom and propose that its ATP synthase genes may function in ATP hydrolysis to maintain a proton gradient between thylakoids and stroma, required by the twin arginine translocator (Tat) system for translocation of particular proteins into thylakoids. Given the correlated retention of ATP synthase genes and genes for the Tat system in distantly related nonphotosynthetic plastids, we suggest that this Tat-related role for ATP synthase was a key constraint during parallel loss of photosynthesis in multiple independent lineages of algae/plants.

Haemosporida parasites of even-toed ungulates are diverse and globally distributed, but since their discovery in 1913 their characterization has relied exclusively on microscopy-based descriptions. In order to bring molecular approaches to bear on the identity and evolutionary relationships of ungulate malaria parasites, we conducted Plasmodium cytb-specific nested PCR surveys using blood from water buffalo in Vietnam and Thailand, and goats in Zambia. We found that Plasmodium is readily detectable from water buffalo in these countries, indicating that buffalo Plasmodium is distributed in a wider region than India, which is the only area in which buffalo Plasmodium has been reported. Two types (I and II) of Plasmodium sequences were identified from water buffalo and a third type (III) was isolated from goat. Morphology of the parasite was confirmed in Giemsa-reagent stained blood smears for the Type I sample. Complete mitochondrial DNA sequences were isolated and used to infer a phylogeny in which ungulate malaria parasites form a monophyletic clade within the Haemosporida, and branch prior to the clade containing bird, lizard and other mammalian Plasmodium. Thus it is likely that host switching of Plasmodium from birds to mammals occurred multiple times, with a switch to ungulates independently from other mammalian Plasmodium.

The unicellular eukaryotic assemblage Discoba (Excavata) comprises four lineages: the Heterolobosea, Euglenozoa, Jakobida, and Tsukubamonadida. Discoba has been considered as a key assemblage for understanding the early evolution of mitochondrial (mt) genomes, as jakobids retain the most gene-rich (i.e., primitive) genomes compared with any other eukaryotes determined to date. However, to date, mt genome sequences have been completed for only a few groups within Discoba, including jakobids, two closely related heteroloboseans, and kinetoplastid euglenozoans. The Tsukubamonadida is the least studied lineage, as the order was only recently established with the description of a sole representative species, Tsukubamonas globosa. The evolutionary relationship between T. globosa and other discobids has yet to be resolved, and no mt genome data are available for this particular organism. Here, we use a “phylogenomic” approach to resolve the relationship between T. globosa, heteroloboseans, euglenozoans, and jakobids. In addition, we have characterized the mt genome of T. globosa (48,463 bp in length), which encodes 52 putative protein-coding and 29 RNA genes. By mapping the gene repertoires of discobid mt genomes onto the well-resolved Discoba tree, we model gene loss events during the evolution of discobid mt genomes.

All members of the order Trypanosomatida known to date are parasites that are most likely descendants of a free-living ancestor. Trypanosomatids are an excellent model to assess the transition from a free-living to a parasitic lifestyle, because a large amount of experimental data has been accumulated for well-studied members that are harmful to humans and livestock (Trypanosoma spp. and Leishmania spp.). However, recent advances in our understanding of the diversity of trypanosomatids and their close relatives (i.e., members of the class Kinetoplastea) have suggested that the change in lifestyle took place multiple times independently from that which gave rise to the extant trypanosomatid parasites. In the current study, transcriptomic data of two parasitic kinetoplastids belonging to orders other than Trypanosomatida, namely Azumiobodo hoyamushi (Neobodonida) and Trypanoplasma borreli (Parabodonida), were generated. We re-examined the transition from a free-living to a parasitic lifestyle in the evolution of kinetoplastids by combining (i) the relationship among the five orders in Kinetoplastea and (ii) that among free-living and parasitic species within the individual orders. The former relationship was inferred from a large-scale multigene alignment including the newly generated data from Azumiobodo and Trypanoplasma, as well as the data from another parasitic kinetoplastid, Perkinsela sp., deposited in GenBank; and the latter was inferred from a taxon-rich small subunit ribosomal DNA alignment. Finally, we discuss the potential value of parasitic kinetoplastids identified in Parabodonida and Neobodonida for studying the evolutionary process that turned a free-living species into a parasite.

In phylogenetic analyses of nucleotide sequences, ‘homogeneous’ substitution models, which assume the stationarity of base composition across a tree, are widely used, albeit individual sequences may bear distinctive base frequencies. In the worst-case scenario, a homogeneous model-based analysis can yield an artifactual union of two distantly related sequences that achieved similar base frequencies in parallel. Such potential difficulty can be countered by two approaches, ‘RY-coding’ and ‘non-homogeneous’ models. The former approach converts four bases into purine and pyrimidine to normalize base frequencies across a tree, while the heterogeneity in base frequency is explicitly incorporated in the latter approach. The two approaches have been applied to real-world sequence data; however, their basic properties have not been fully examined by pioneering simulation studies. Here, we assessed the performances of the maximum-likelihood analyses incorporating RY-coding and a non-homogeneous model (RY-coding and non-homogeneous analyses) on simulated data with parallel convergence to similar base composition. Both RY-coding and non-homogeneous analyses showed superior performances compared with homogeneous model-based analyses. Curiously, the performance of RY-coding analysis appeared to be significantly affected by a setting of the substitution process for sequence simulation relative to that of non-homogeneous analysis. The performance of a non-homogeneous analysis was also validated by analyzing a real-world sequence data set with significant base heterogeneity.