Yonas I. Tekle

Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny

A principal objective for phylogenetic experimental design is to predict the power of a data set to resolve nodes in a phylogenetic tree. However, proactively assessing the potential for phylogenetic noise compared with signal in a candidate data set has been a formidable challenge. Understanding the impact of collection of additional sequence data to resolve recalcitrant internodes at diverse historical times will facilitate increasingly accurate and cost-effective phylogenetic research. Here, we derive theory based on the fundamental unit of the phylogenetic tree, the quartet, that applies estimates of the state space and the rates of evolution of characters in a data set to predict phylogenetic signal and phylogenetic noise and therefore to predict the power to resolve internodes. We develop and implement a Monte Carlo approach to estimating power to resolve as well as deriving a nearly equivalent faster deterministic calculation. These approaches are applied to describe the distribution of potential signal, polytomy, or noise for two example data sets, one recent (cytochrome c oxidase I and 28S ribosomal rRNA sequences from Diplazontinae parasitoid wasps) and one deep (eight nuclear genes and a phylogenomic sequence for diverse microbial eukaryotes including Stramenopiles, Alveolata, and Rhizaria). The predicted power of resolution for the loci analyzed is consistent with the historic use of the genes in phylogenetics.

Multigene Evidence for the Placement of a Heterotrophic Amoeboid Lineage Leukarachnion sp. among Photosynthetic Stramenopiles

The colorless amoeboid eukaryote genus Leukarachnion represents one of a long list of microbial lineages for which there have been few taxonomic studies. In this study, we analyze molecular data to assess the placement of a species of Leukarachnion on the eukaryotic tree of life and we report fine structural data to provide additional information on the identity of this taxon. Our multigene analyses indicate that Leukarachnion sp. (ATCC PRA-24) is a member of the stramenopiles, sister to the Chrysophyceae/Synurophyceae clade. It also forms a sister group relationship to the clade containing Chlamydomyxa labyrinthuloides and Synchroma grande, both of which are characterized by net-like amoeboid phases. Leukarachnion sp. and Chlamydomyxa labyrinthuloides also share fine structural cyst morphology such as bilayered structure of the cyst wall. The amoeboid form and heterotrophic habit of Leukarachnion sp. highlight the multiple origins of diverse body forms and multiple plastid losses within the stramenopiles.

Molecular Data Are Transforming Hypotheses on the Origin and Diversification of Eukaryotes

The explosion of molecular data has transformed hypotheses on both the origin of eukaryotes and the structure of the eukaryotic tree of life. Early ideas about the evolution of eukaryotes arose through analyses of morphology by light microscopy and, later, electron microscopy. Though such studies have proven powerful at resolving more recent events, theories on origins and diversification of eukaryotic life have been substantially revised in light of analyses of molecular data including gene and, increasingly, whole-genome sequences. By combining these approaches, progress has been made in elucidating the origin and diversification of eukaryotes. Yet many aspects of the evolution of eukaryotic life remain to be illuminated.

Epidemiological game-theory dynamics of chickenpox vaccination in the USA and Israel

The general consensus from epidemiological game-theory studies is that vaccination coverage driven by self-interest (Nash vaccination) is generally lower than group-optimal coverage (utilitarian vaccination). However, diseases that become more severe with age, such as chickenpox, pose an exception to this general consensus. An individual choice to be vaccinated against chickenpox has the potential to harm those not vaccinated by increasing the average age at infection and thus the severity of infection as well as those already vaccinated by increasing the probability of breakthrough infection. To investigate the effects of these externalities on the relationship between Nash and utilitarian vaccination coverages for chickenpox, we developed a game-theory epidemic model that we apply to the USA and Israel, which has different vaccination programmes, vaccination and treatment costs, as well as vaccination coverage levels. We find that the increase in chickenpox severity with age can reverse the typical relationship between utilitarian and Nash vaccination coverages in both the USA and Israel. Our model suggests that to obtain herd immunity of chickenpox vaccination, subsidies or external regulation should be used if vaccination costs are high. By contrast, for low vaccination costs, improving awareness of the vaccine and the potential cost of chickenpox infection is crucial.

Identification of new molecular markers for assembling the eukaryotic tree of life

Six eukaryotic supergroups have been proposed based on both morphological and molecular data. However, some of these supergroups are contentious and the deep relationships among them are poorly resolved. This is due to a limited number of morphological characters and few molecular markers in current use. The lack of resolution in most multigene analyses, including phylogenomic analyses, necessitates a search for additional, appropriate molecular markers to enable targeted sampling of taxa in key phylogenetic positions. We evaluated the phylogenetic signal of 860 proteins obtained from the Clusters of Orthologous Groups of proteins (COGs) database. We report a total of 17 markers that resulted in well-resolved topologies that are congruent with well-established components of the eukaryotic tree. To establish their utility, we designed universal degenerate primers for six markers, some of which showed promising results in unicellular eukaryotes. Finally, we present phylogenetic informativeness profiles for seven selected markers, revealing that the markers contain phylogenetic signal that spans the whole tree including the deeper branches.

A Description of a New ''Amoebozoan'' Isolated from the American Lobster, Homarus americanus

ABSTRACT. Our knowledge of the diversity of amoeboid protists is rapidly expanding as new and old habitats are more fully explored. In 2003, while investigating the cause of an amoeboid disease afflicting lobsters on the East Coast, samples were examined for the presence of amoebae from the carapace washings of the American lobster, Homarus americanus. During this survey a unique community of gymnamoebae was discovered. Among the new taxa discovered was a small Thecamoeba‐like organism with a single posteriorly directed pseudopodium. Although resembling Parvamoeba rugata, this amoeba displayed distinctive morphology from that isolate or any other amoebozoan. Phylogenetic analysis shows this amoeba is distantly related to the Thecamoebidae. In this paper we describe the unique morphology of a second species of Parvamoeba and discuss its phylogenetic position with respect to the “Amoebozoa.”

DNA barcoding in amoebozoa and challenges: the example of Cochliopodium.

The diversity of microbial eukaryotes in general and amoeboid lineages in particular is poorly documented. Even though amoeboid lineages are among the most abundant microbes, taxonomic progress in the group has been hindered by the limitations of traditional taxonomy and technical difficultly in studying them. Studies using molecular approaches such as DNA barcoding with cytochrome oxidase I (COI) gene are slowly trickling in for Amoebozoa, and they hopefully will aid in unveiling the true diversity of the group. In this study a retrospective approach is used to test the utility of COI gene in a scale-bearing amoeba, Cochliopodium, which is morphologically well defined. A total of 126 COI sequences and 62 unique haplotypes were generated from 9 Cochliopodium species. Extensive analyses exploring effects of sequence evolution models and length of sequence on genetic diversity computations were conducted. The findings show that COI is a promising marker for Cochliopodium, except in one case where it failed to delineate two morphologically well-defined cochliopodiums. Two species delimitation approaches also recognize 8 genetic lineages out of 9 species examined. The taxonomic implications of these findings and factors that may confound COI as a barcode marker in Cochliopodium and other amoebae are discussed.

A New Freshwater Amoeba: Cochliopodium pentatrifurcatum n. sp. (Amoebozoa, Amorphea)

Cochliopodium pentatrifurcatum n. sp. (ATCC© 30935TM) is described based on light microscopic morphology, fine structure, and molecular genetic evidence. Cochliopodium pentatrifurcatum n. sp. (length ~ 25 μm) is characterized by surface microscales (0.3 μm tall) containing a circular porous base (~ 0.6 μm diam.) with a thin peripheral rim. Five radially arranged feet, emanating from the base, support a short central column terminating apically as a funnel‐shaped collar (~ 0.5 μm diam.) composed of five radial, trifurcate rays extending from the center toward a thin peripheral rim. The central spine is 0.5–0.6 μm long. The comparative morphologies and combined molecular genetic evidence, SSU‐rDNA and COI, indicate that the new species falls in a clade sufficiently different from other species to suggest that it is a valid new species.

Controlling Antimicrobial Resistance through Targeted, Vaccine-Induced Replacement of Strains

Vaccination has proven effective in controlling many infectious diseases. However, differential effectiveness with regard to pathogen genotype is a frequent reason for failures in vaccine development. Often, insufficient immune response is induced to prevent infection by the diversity of existing serotypes present in pathogenic populations of bacteria. These vaccines that target a too narrow spectrum of serotypes do not offer sufficient prevention of infections, and can also lead to undesirable strain replacements. Here, we examine a novel idea to specifically exploit the narrow spectrum coverage of some vaccines to combat specific, emerging multi- and pan-resistant strains of pathogens. Application of a narrow-spectrum vaccine could serve to prevent infections by some strains that are hard to treat, rather than offer the vaccinated individual protection against infections by the pathogenic species as such. We suggest that vaccines targeted to resistant serotypes have the potential to become important public health tools, and would represent a new approach toward reducing the burden of particular multi-resistant strains occurring in hospitals. Vaccines targeting drug-resistant serotypes would also be the first clinical intervention with the potential to drive the evolution of pathogenic populations toward drug-sensitivity. We illustrate the feasibility of this approach by modeling a hypothetical vaccine that targets a subset of methicillin-resistant Staphylococcus aureus (MRSA) genotypes, in combination with drug treatment targeted at drug-sensitive genotypes. We find that a combined intervention strategy can limit nosocomial outbreaks, even when vaccine efficacy is imperfect. The broader utility of vaccine-based resistance control strategies should be further explored taking into account population structure, and the resistance and transmission patterns of the pathogen considered.

Evidence of parasexual activity in "asexual amoebae" Cochliopodium spp. (Amoebozoa): extensive cellular and nuclear fusion.

The majority of microbial eukaryotes have long been considered asexual, though new evidence indicates sex, or sexual-like (parasexual) behaviors that deviate from the usual union of two gametes, among other variant aspects. Over a dozen amoebozoans are implicated to have sexual stages. However, the exact mechanism by which sex occurs in these lineages remains elusive. This is mainly due to the diverse quality and cryptic nature of their life cycle. In this study we present evidence of some previously unreported aspects of the life cycle of an amoeba, Cochliopodium, that undergoes unusual intraspecific interactions using light microscopy and immunocytochemistry. Similar to other amoebozoans, Cochliopodium, is considered asexual with no published reports of sex or parasexuality. We also investigated environmental conditions that govern the observed intraspecific interactions. Both light microscopic and immunocytochemistry evidence demonstrates Cochliopodium undergoes cellular fusion (plasmogamy) and nuclear fusion (karyogamy). Large plasmodia eventually undergo karyogamy and contain large fused, polyploid, nuclei. These are observed to fragment, subsequently, by karyotomy (nuclear fission) and cytoplasmic fission to yield uninucleated amoebae. This process could lead to a non-meiotic, parasexual exchange of chromosomes in Cochliopodium. These findings strongly suggest that Cochliopodium is involved in parasexual activity and should no longer be considered strictly asexual.