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

A Description of Cochliopodium megatetrastylus n. sp. Isolated from a Freshwater Habitat

Cochliopodium megatetrastylus n. sp. is described based on light microscopy, fine structure and molecular genetic evidence. Amoebae are broadly oval to somewhat triangular during locomotion with average length of 37 μm and breadth of 50 μm, and surrounded by a hyaloplasm margin, somewhat narrow when at rest but more expanded during locomotion (~ 5–10 μm at the anterior). Sparsely occurring subpseudopodia, barely emergent from the hyaloplasm, are blunt and finger-like, occasionally becoming adhesive laterally or at the posterior. Cysts develop after 2–3 weeks in culture and are round with a distinct margin, decreasing in size from 20 to 5 μm during maturation. The granuloplasm contains refractile crystals. A vesicular nucleus (~ 6 μm), containing a nucleolus (2–3 μm), is variable in shape from somewhat lenticular in section to irregularly rounded with undulating or lobed margins. Surface scales (~ 0.3 μm in height) have an apical deeply concave funnel-like collar (~ 0.15 μm deep), without a spine, composed of radial fine rays and concentric filaments forming a finemesh, supported on four non-cross-linked styles (~ 0.2 μm apart) attached to a round to broadly angular base plate (0.6–1 μm) with a fine gridtexture. Cysts are rounded and enclosed by an organic wall bearing remnants of the scales on its outer surface. Both concatenated analysis of SSU-rDNA and COI genes and comparative morphologies support the designation of Cochliopodium megatetrastylus n. sp. as a new species

Broadly Sampled Multigene Trees of Eukaryotes

Background. Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the \u27Amoebozoa\u27, \u27Chromalveolata\u27, \u27Excavata\u27, \u27Opisthokonta\u27, \u27Plantae\u27, and \u27Rhizaria\u27. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2) to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches. Results. The inferred trees reveal strong support for many clades that also have defining ultrastructural or molecular characters. In contrast, we find limited to no support for most of the putative supergroups as only the \u27Opisthokonta\u27 receive strong support in our analyses. The supergroup \u27Amoebozoa\u27 has only moderate support, whereas the \u27Chromalveolata\u27, \u27Excavata\u27, \u27Plantae\u27, and \u27Rhizaria\u27 receive very limited or no support. Conclusion. Our analytical approach substantiates the power of increased taxon sampling in placing diverse eukaryotic lineages within well-supported clades. At the same time, this study indicates that the six supergroup hypothesis of higher-level eukaryotic classification is likely premature. The use of a taxon-rich data set with 105 lineages, which still includes only a small fraction of the diversity of microbial eukaryotes, fails to resolve deeper phylogenetic relationships and reveals no support for four of the six proposed supergroups. Our analyses provide a point of departure for future taxon- and gene-rich analyses of the eukaryotic tree of life, which will be critical for resolving their phylogenetic interrelationships

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Systematic Biology 59 (2010): 518-533, doi:10.1093/sysbio/syq037.An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ‘Chromalveolata’ is rejected. Further, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxonrich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data

A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes

Abstract Background Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogenomic studies to infer ancient evolutionary histories. However, its utility in studying cryptic species diversity is not well explored. An empirical investigation was conducted to test the applicability of transcriptome data in resolving two major types of discordances at lower taxonomic levels. These include cases where species have the same morphology but different genetics (cryptic species) and species of different morphologies but have the same genetics. We built a species comparison bioinformatic pipeline that takes into account the nature of transcriptome data in amoeboid microbes exemplifying such discordances. Result Our analyses of known or suspected cryptic species yielded consistent results regardless of the methods of culturing, RNA collection or sequencing. Over 95% of the single copy genes analyzed in samples of the same species sequenced using different methods and cryptic species had intra- and interspecific divergences below 2%. Only a minority of groups (2.91–4.87%) had high distances exceeding 2% in these taxa, which was likely caused by low data quality. This pattern was also observed in suspected genetically similar species with different morphologies. Transcriptome data consistently delineated all taxa above species level, including cryptically diverse species. Using our approach we were able to resolve cryptic species problems, uncover misidentification and discover new species. We also identified several potential barcode markers with varying evolutionary rates that can be used in lineages with different evolutionary histories. Conclusion Our findings demonstrate that transcriptome data is appropriate for understanding cryptic species diversity in microbial eukaryotes

A Description of Cochliopodium megatetrastylus n. sp. Isolated from a Freshwater Habitat

Cochliopodium megatetrastylus n. sp. is described based on light microscopy, fine structure and molecular genetic evidence. Amoebae are broadly oval to somewhat triangular during locomotion with average length of 37 μm and breadth of 50 μm, and surrounded by a hyaloplasm margin, somewhat narrow when at rest but more expanded during locomotion (~ 5–10 μm at the anterior). Sparsely occurring subpseudopodia, barely emergent from the hyaloplasm, are blunt and finger-like, occasionally becoming adhesive laterally or at the posterior. Cysts develop after 2–3 weeks in culture and are round with a distinct margin, decreasing in size from 20 to 5 μm during maturation. The granuloplasm contains refractile crystals. A vesicular nucleus (~ 6 μm), containing a nucleolus (2–3 μm), is variable in shape from somewhat lenticular in section to irregularly rounded with undulating or lobed margins. Surface scales (~ 0.3 μm in height) have an apical deeply concave funnel-like collar (~ 0.15 μm deep), without a spine, composed of radial fine rays and concentric filaments forming a finemesh, supported on four non-cross-linked styles (~ 0.2 μm apart) attached to a round to broadly angular base plate (0.6–1 μm) with a fine gridtexture. Cysts are rounded and enclosed by an organic wall bearing remnants of the scales on its outer surface. Both concatenated analysis of SSU-rDNA and COI genes and comparative morphologies support the designation of Cochliopodium megatetrastylus n. sp. as a new species

Data from: 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 dataset to resolve nodes in a phylogenetic tree. However, proactively assessing the potential for phylogenetic noise compared to signal in a candidate dataset 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 dataset 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 datasets, one recent (CO1 and 28S 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

Differential gene expression analysis and cytological evidence reveal a sexual stage of an amoeba with multiparental cellular and nuclear fusion.

Sex is a hallmark of eukaryotes but its evolution in microbial eukaryotes is poorly elucidated. Recent genomic studies revealed microbial eukaryotes possess a genetic toolkit necessary for sexual reproduction. However, the mechanism of sexual development in a majority of microbial eukaryotes including amoebozoans is poorly characterized. The major hurdle in studying sex in microbial eukaryotes is a lack of observational evidence, primarily due to its cryptic nature. In this study, we used a tractable fusing amoeba, Cochliopodium, to investigate sexual development using stage-specific Differential Gene Expression (DGE) and cytological analyses. Both DGE and cytological results showed that most of the meiosis and sex-related genes are upregulated in Cochliopodium undergoing fusion in laboratory culture. Relative gene ontology (GO) category representations in unfused and fused cells revealed a functional skew of the fused transcriptome toward DNA metabolism, nucleus and ligases that are suggestive of a commitment to sexual development. However, the GO categories of unfused cells were dominated by metabolic pathways and other processes indicative of a vegetative phase. Our study provides strong evidence that the fused cells represent a sexual stage in Cochliopodium. Our findings have further implications in understanding the evolution and mechanism of inheritance involving multiparents in other eukaryotes with a similar reproductive strategy

Table S1: Deep microbial eukaryote sequences.

Table S1: Deep microbial eukaryote sequences