The tree of eukaryotes

Keeling, Patrick J.; Burger, Gertraud; Durnford, Dion G.; Lang, B. Franz; Lee, William R.; Pearlman, Ronald E.; Roger, Andrew J.; Gray, Michael W.

doi:10.1016/j.tree.2005.09.005

Cited by 529 publications

(387 citation statements)

References 76 publications

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“…The most recent conceptions of the eukaryotic tree of life feature five or six "supergroups" (Keeling et al 2005;Roger and Simpson 2009;Burki 2014) including Opisthokonta, Amoebozoa, Excavata, the SAR group, Archaeplastida, and Hacrobia (Haptophyta and Cryptophyta). Whereas phylogenomic analyses robustly recover the monophyly of Opisthokonta, Amoebozoa and SAR, the phylogenetic coherence of Excavata, Archaeplastida, and Hacrobia is less certain (see also Fig.…”

Section: The Eukaryotic Tree Of Lifementioning

confidence: 99%

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

Eme

Sharpe

Brown

et al. 2014

Cold Spring Harbor Perspectives in Biology

209

145

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Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossilcalibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655 -2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.

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Section: The Eukaryotic Tree Of Lifementioning

confidence: 99%

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

Eme

Sharpe

Brown

et al. 2014

Cold Spring Harbor Perspectives in Biology

209

145

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“…The phytoplankton responsible for marine primary production include the cyanobacteria, Prochlorococcus and Synechococcus, and a multitude of eukaryotic phytoplankton, such as diatoms, dinoflagellates, prasinophytes, and prymnesiophytes (2)(3)(4). Most oceanic phytoplankton are "picoplanktonic" (<2-3 μm diameter) and have high surface area to volume ratios, an advantage in open-ocean low-nutrient conditions (5)(6)(7)(8).…”

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confidence: 99%

“…Six picoplanktonic prymnesiophytes exist in culture (6, 7) but prymnesiophyte 18S rDNA sequences from <2-3-μm size-fractioned environmental samples typically belong to uncultured taxa (6,(13)(14)(15). As a whole, this lineage reportedly diverged from other major eukaryotic lineages early on, 1.2 billion years ago (16), and their overall placement among eukaryotes is uncertain (4,16). They are extremely distant from phytoplankton with published genomes.…”

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confidence: 99%

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

Cuvelier

Allen

Monier

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

262

267

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Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa, however, are not well known, and genomes have been analyzed from only the latter two lineages. Tiny "picoplanktonic" members of the prymnesiophyte lineage have long been inferred to be ecologically important but remain poorly characterized. Here, we examine pico-prymnesiophyte evolutionary history and ecology using cultivation-independent methods. 18S rRNA gene analysis showed picoprymnesiophytes belonged to broadly distributed uncultivated taxa. Therefore, we used targeted metagenomics to analyze uncultured pico-prymnesiophytes sorted by flow cytometry from subtropical North Atlantic waters. The data reveal a composite nuclear-encoded gene repertoire with strong green-lineage affiliations, which contrasts with the evolutionary history indicated by the plastid genome. Measured pico-prymnesiophyte growth rates were rapid in this region, resulting in primary production contributions similar to the cyanobacterium Prochlorococcus. On average, picoprymnesiophytes formed 25% of global picophytoplankton biomass, with differing contributions in five biogeographical provinces spanning tropical to subpolar systems. Elements likely contributing to success include high gene density and genes potentially involved in defense and nutrient uptake. Our findings have implications reaching beyond pico-prymnesiophytes, to the prasinophytes and stramenopiles. For example, prevalence of putative Ni-containing superoxide dismutases (SODs), instead of Fe-containing SODs, seems to be a common adaptation among eukaryotic phytoplankton for reducing Fe quotas in low-Fe modern oceans. Moreover, highly mosaic gene repertoires, although compositionally distinct for each major eukaryotic lineage, now seem to be an underlying facet of successful marine phytoplankton.comparative genomics | primary production | prymnesiophytes | marine photosynthesis | haptophytes G lobal primary production is partitioned equally among terrestrial and marine ecosystems, each accounting for ≈50 gigatons of carbon per year (1). The phytoplankton responsible for marine primary production include the cyanobacteria, Prochlorococcus and Synechococcus, and a multitude of eukaryotic phytoplankton, such as diatoms, dinoflagellates, prasinophytes, and prymnesiophytes (2-4). Most oceanic phytoplankton are "picoplanktonic" (<2-3 μm diameter) and have high surface area to volume ratios, an advantage in open-ocean low-nutrient conditions (5-8). Despite the importance of eukaryotic phytoplankton to carbon cycling only six genomes have been sequenced and analyzed comparatively, all being from diatoms and prasinophytes. These revealed greater differentiation than anticipated on the basis of 18S rRNA gene analyses (9-11). The observed genomic divergence is associated with major differences in physiology and niche adaptation (10).Pigment-based estimates indicate that prymnesiophytes, also know...

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“…The group contains approximately 6,000 named species, with perhaps only 0.1 % of the species having been named to date (Adl et al, 2007), many of which are pathogens of humans and domesticated animals. The phylum is now recognized as being closely related to the dinoflagellates and ciliates (forming the taxonomic group Alveolata), and less closely to the stramenopiles (forming the group Chromalveolata) (Simpson & Roger, 2004;Adl et al, 2005;Keeling et al, 2005). Apicomplexa is traditionally considered to contain four clearly defined groups (Adl et al, 2005): the coccidians, the gregarines, the haemosporidians, and the piroplasms.…”

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confidence: 99%

Prospects for elucidating the phylogeny of the Apicomplexa

2008

Parasite

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Summary :The Apicomplexa is traditionally considered to contain four clearly defined groups, but the phylogenetic relationships among these groups, and their subsequent taxonomic arrangement, are currently unclear. Here, I consider five of the important criteria that need to be met before radical taxonomic changes are made, in relation to phylogenetic analyses. Unfortunately, at least four of these criteria indicate that the prospects for elucidating the phylogeny and taxonomy of the Apicomplexa are not good in the short term. A lot more pertinent data need to be collected, both in terms of taxa sampled and genes sequenced, before any concordance among phylogenies is likely to emerge; and someone (e.g. a consortium) needs to co-ordinate the active collection and analysis of these data if any worthwhile progress is to be made.

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The tree of eukaryotes

Cited by 529 publications

References 76 publications

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

Prospects for elucidating the phylogeny of the Apicomplexa

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