Approximating model probabilities in Bayesian information criterion and decision-theoretic approaches to model selection in phylogenetics

Distribution and Functional Analysis of Isocitrate Dehydrogenases across Kinetoplastids

Isocitrate dehydrogenase is an enzyme converting isocitrate to α-ketoglutarate in the canonical tricarboxylic acid (TCA) cycle. There are three different types of isocitrate dehydrogenase documented in eukaryotes. Our study points out the complex evolutionary history of isocitrate dehydrogenases across kinetoplastids, where the common ancestor of Trypanosomatidae and Bodonidae was equipped with two isoforms of the isocitrate dehydrogenase enzyme: the NADP+-dependent isocitrate dehydrogenase 1 with possibly dual localization in the cytosol and mitochondrion and NADP+-dependent mitochondrial isocitrate dehydrogenase 2. In the extant trypanosomatids, isocitrate dehydrogenase 1 is present only in a few species suggesting that it was lost upon separation of Trypanosoma spp. and replaced by the mainly NADP+-dependent cytosolic isocitrate dehydrogenase 3 of bacterial origin in all the derived lineages. In this study, we experimentally demonstrate that the omnipresent isocitrate dehydrogenase 2 has a dual localization in both mitochondrion and cytosol in at least four species that possess only this isoform. The apparent lack of the NAD+-dependent isocitrate dehydrogenase activity in trypanosomatid mitochondrion provides further support to the existence of the noncanonical TCA cycle across trypanosomatids and the bidirectional activity of isocitrate dehydrogenase 3 when operating with NADP+ cofactor instead of NAD+. This observation can be extended to all 17 species analyzed in this study, except for Leishmania mexicana, which showed only low isocitrate dehydrogenase activity in the cytosol. The variability in isocitrate oxidation capacity among species may reflect the distinct metabolic strategies and needs for reduced cofactors in particular environments.

Leishmania guyanensis M4147 as a new LRV1-bearing model parasite: Phosphatidate phosphatase 2-like protein controls cell cycle progression and intracellular lipid content

Leishmaniasis is a parasitic vector-borne disease caused by the protistan flagellates of the genus Leishmania. Leishmania (Viannia) guyanensis is one of the most common causative agents of the American tegumentary leishmaniasis. It has previously been shown that L. guyanensis strains that carry the endosymbiotic Leishmania RNA virus 1 (LRV1) cause more severe form of the disease in a mouse model than those that do not. The presence of the virus was implicated into the parasite's replication and spreading. In this respect, studying the molecular mechanisms of cellular control of viral infection is of great medical importance. Here, we report ~30.5 Mb high-quality genome assembly of the LRV1-positive L. guyanensis M4147. This strain was turned into a model by establishing the CRISPR-Cas9 system and ablating the gene encoding phosphatidate phosphatase 2-like (PAP2L) protein. The orthologue of this gene is conspicuously absent from the genome of an unusual member of the family Trypanosomatidae, Vickermania ingenoplastis, a species with mostly bi-flagellated cells. Our analysis of the PAP2L-null L. guyanensis showed an increase in the number of cells strikingly resembling the bi-flagellated V. ingenoplastis, likely as a result of the disruption of the cell cycle, significant accumulation of phosphatidic acid, and increased virulence compared to the wild type cells.

Localized Outbreaks of Epidemic Polyarthritis among Military Personnel Caused by Different Sublineages of Ross River Virus, Northeastern Australia, 2016-2017

Two outbreaks of epidemic polyarthritis occurred among Australian Defence Force personnel during and following short military exercises in the Shoalwater Bay Training Area, northeastern Australia, in 2016 and 2017. Ross River virus (RRV) IgM was detected in acute-phase serum samples from most patients (28/28 in 2016 and 25/31 in 2017), and RRV was recovered from 4/38 serum samples assayed (1/21 in 2016 and 3/17 in 2017). Phylogenetic analyses of RRV envelope glycoprotein E2 and nonstructural protein nsP3 nucleotide sequences segregated the RRV isolates obtained in 2016 and 2017 outbreaks into 2 distinct sublineages, suggesting that each outbreak was caused by a different strain of RRV. The spatiotemporal characteristics of the 2016 outbreak suggested that some of the infections involved human-mosquito-human transmission without any intermediate host. These outbreaks highlight the importance of personal protective measures in preventing vectorborne diseases for which no vaccine or specific prophylaxis exists.

Phylogenetic inference for the study of within-host HIV-1 dynamics and persistence on antiretroviral therapy

Although antiretroviral therapy (ART) is highly effective at inhibiting HIV-1 replication and preventing AIDS, it cannot eradicate the infection. Many studies have used viral genetic information from single-genome and deep sequencing of blood and tissue samples to investigate the mechanisms that sustain the HIV-1 reservoir. Sequence data are analysed by use of measurements of population diversity and divergence and by exploration of phylogenetic associations. The study of intrahost HIV-1 populations on ART requires specific considerations as their dynamics can be shaped by host factors such as cell death and proliferation. Hence, understanding both the biology of HIV-1 persistence and the phylogenetic methods that can be applied to this field is crucial. We conclude that the most suitable phylogenetic methods and evolutionary models for characterising HIV-1 populations on ART include using neighbour-joining trees to identify identical proviral sequences that might result from T-cell proliferation, and using maximum-likelihood analysis to investigate the possibility of ongoing viral replication on ART. Characterising the reservoir for HIV-1 on ART is a high priority for the design of curative interventions.

A Not-So-Long Introduction to Computational Molecular Evolution

In this chapter, we give a not-so-long and self-contained introduction to computational molecular evolution. In particular, we present the emergence of the use of likelihood-based methods, review the standard DNA substitution models, and introduce how model choice operates. We also present recent developments in inferring absolute divergence times and rates on a phylogeny, before showing how state-of-the-art models take inspiration from diffusion theory to link population genetics, which traditionally focuses at a taxonomic level below that of the species, and molecular evolution. Although this is not a cookbook chapter, we try and point to popular programs and implementations along the way.

Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias)

Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here, we investigate extensive mtDNA introgression in western chipmunks, focusing on species in the Tamias quadrivittatus group from the central and southern Rocky Mountains. Specifically, we investigate the role of selection in driving patterns of introgression. We sequenced 51 mtDNA genomes from six species and combine these sequences with other published genomic data to yield annotated mitochondrial reference genomes for nine species of chipmunks. Genomic characterization was performed using a series of molecular evolutionary and phylogenetic analyses to test protein-coding genes for positive selection. We fit a series of maximum likelihood models using a model-averaging approach, assessed deviations from neutral expectations, and performed additional tests to search for codons under the influence of selection. We found no evidence for positive selection among these genomes, suggesting that selection has not been the driving force of introgression in these species. Thus, extensive mtDNA introgression among several species of chipmunks likely reflects genetic drift of introgressed alleles in historically fluctuating populations.

The essentials of computational molecular evolution

In this chapter, we give a brief yet self-contained introduction to computational molecular evolution. In particular, we present the emergence of the use of likelihood-based methods, review the standard DNA substitution models, and introduce how model choice operates. We also present recent developments in inferring absolute dates and rates on a phylogeny and show how state-of-the-art models take inspiration from diffusion theory to link population genetics, which traditionally focuses at a taxonomic level under that of species, and molecular evolution.