| 1. |
- Adl, Sina M., et al.
(author)
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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
- 2019
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In: Journal of Eukaryotic Microbiology. - : WILEY. - 1066-5234 .- 1550-7408. ; 66:1, s. 4-119
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Journal article (peer-reviewed)abstract
- This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.
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| 2. |
- Al Jewari, Caesar
(author)
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Resolving deep nodes of eukaryote phylogeny
- 2022
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Doctoral thesis (other academic/artistic)abstract
- My thesis aims to solve deep nodes in the eukaryote tree of life (eToL), by developing new data sets and new approaches to analysing them. In paper I, I described a dataset of 76 universal eukaryotic proteins of bacterial descent (euBacs), in order to test the relations among the three main divisions of mitochondriate eukaryotes (Amorphea, Diaphretickes and Discoba). I developed two protocols to identify problematic data. The conJac protocol analyzes data by jackknifing to detect outlier sequences, while conWin uses a sliding window to find sequence fragments of potentially foreign origin. Phylogenetic analyses of the 76 euBacs, with and without conWin or conJac filtering place Discoba as the sister group to Amorphea and Diaphretickes. The results are largely consistent and highly supported under various evolutionary models except for highly complex CAT models. In paper II, I describe a dataset of 198 universal eukaryote proteins of archaeal ancestry (euArcs), which includes the remaining eukaryotes, informally referred to as amitochondriate excavate. These were excluded from the previous study because they lack euBacs. Phylogenetic analyses of the euArc dataset place the amitochondriate excavate as the first three branches of eToL, followed by Discoba, the only mitochondriate excavates, which appear as a sister group to the remaining eukaryotes. I also developed a protocol using predicted protein structures to increase the fitness of the model without inflating the parameter space, allowing me to conduct a series of control analyses and further support the multi-excavate root. In Paper III, I describe a new application of reciprocal-rooting using concatenated sequences, which I then use to test the euArc root. I also developed two sampling protocols unique to this kind of data. The protocols confirm the multi-excavate euArc root, which indicates that eukaryotes arose from an excavate ancestor. Paper IV describes a follow-up on the ConWin results from Paper I. These show moderate to strong support for mosaicism in 16 euBac proteins from diverse metabolic pathways and donor lineages. In summary, this thesis presents a novel root for the eukaryote tree of life. The new root requires revision of fundamental theories of eukaryote evolution including the source and timing of mitochondrial origins. The methods I have developed are applicable to many different kinds of phylogenetic studies, and the new protein structure model should make these analyses faster, more flexible, and more widely available.
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| 3. |
- Alfjorden, Anders, et al.
(author)
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Identification of a new gregarine parasite [Apicomplexa, Alveolata] in mass mortality events of freshwater pearl mussels (Margaritifera margaritifera)
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Other publication (other academic/artistic)abstract
- The freshwater pearl mussel (FPM) Margaritifera margaritifera is a Holarctic species with key roles in river ecosystems. Although of highly ecological importance the species is globally threatened and reaching nearing extinction in Europe. FPM is particularly vulnerable to fluctuations of environmental conditions, being entirely dependent of highly oxygenated streams with clear running water. Therefore anthropogenic activities resulting in habitat loss or affecting water quality such as sedimentation, eutrophication, or acidification of streams have been viewed as important causes of the mass mortality events in FPM. However, in many of these investigations, possible infections from protist parasites were never considered. Here report on a novel parasite associated with several population losses in Swedish rivers. Phylogenetic analysis of the first molecular data for this parasite (18S rDNA gene) revealed that it is related to a terrestrial group of gregarines (Apicomplexa), specifically to parasites of tadpoles belonging to the genus Nematopsis. Further investigations of environmental data revealed the presence of this parasite in Canadian peat bogs and Swedish lakes. We describe the parasite using histology, in-situ hybridization, and transmission electron microscopy and propose a tentative life cycle within the FPM host. Together, our results identify for the first time a pathogenic agent that maybe responsible for the steady decline of a critical animal species in freshwater ecosystems worldwide.
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| 4. |
- Alfjorden, Anders, et al.
(author)
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Identification of a new gregarine parasite associated with mass mortality events of freshwater pearl mussels (Margaritifera margaritifera) in Sweden
- 2024
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In: JOURNAL OF EUKARYOTIC MICROBIOLOGY. - 1066-5234 .- 1550-7408.
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Journal article (peer-reviewed)abstract
- Freshwater bivalves play key ecological roles in lakes and rivers, largely contributing to healthy ecosystems. The freshwater pearl mussel, Margaritifera margaritifera, is found in Europe and on the East coast of North America. Once common in oxygenated streams, M. margaritifera is rapidly declining and consequently assessed as a threatened species worldwide. Deterioration of water quality has been considered the main factor for the mass mortality events affecting this species. Yet, the role of parasitic infections has not been investigated. Here, we report the discovery of three novel protist lineages found in Swedish populations of M. margaritifera belonging to one of the terrestrial groups of gregarines (Eugregarinorida, Apicomplexa). These lineages are closely related-but clearly separated-from the tadpole parasite Nematopsis temporariae. In one lineage, which is specifically associated with mortality events of M. margaritifera, we found cysts containing single vermiform zoites in the gills and other organs of diseased individuals using microscopy and in situ hybridization. This represents the first report of a parasitic infection in M. margaritifera that may be linked to the decline of this mussel species. We propose a tentative life cycle with the distribution of different developmental stages and potential exit from the host into the environment.
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| 5. |
- Bass, David, et al.
(author)
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Ascetosporea
- 2019
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In: Current Biology. - : CELL PRESS. - 0960-9822 .- 1879-0445. ; 29:1, s. R7-R8
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Journal article (other academic/artistic)
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| 6. |
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| 7. |
- Burki, Fabien, et al.
(author)
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Diversity and ecology of protists revealed by metabarcoding
- 2021
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In: Current Biology. - : Cell Press. - 0960-9822 .- 1879-0445. ; 31:19, s. R1267-R1280
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Research review (peer-reviewed)abstract
- Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach.
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| 8. |
- Burki, Fabien
(author)
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Mitochondrial Evolution : Going, Going, Gone
- 2016
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In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 26:10, s. R410-R412
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Journal article (other academic/artistic)abstract
- Monocercomonoides is the first example of a eukaryote lacking even the most reduced form of a mitochondrion-related organelle. This has important implications for cellular processes and our understanding of reductive mitochondrial evolution across the eukaryotic tree of life.
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| 9. |
- Burki, Fabien
(author)
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The Convoluted Evolution of Eukaryotes With Complex Plastids
- 2017
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In: Secondary Endosymbioses. - : Elsevier. - 9780128026519 ; , s. 1-30
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Book chapter (other academic/artistic)abstract
- The textbook version of how plastids were established by endosymbiosis and subsequently diversified is like a well-oiled machine: a cyanobacterial endosymbiont was taken up by a heterotrophic cell and transformed over time into a bona fide photosynthetic organelle (plastid), ultimately giving rise to all plants and algae. The reality, however, is much more complicated and this chapter attempts to describe recent advances in the field of plastid evolution brought to light by disciplines such as phylogenomics, comparative genomics, and cell biology. If (almost) all plastids may ultimately trace back to the same original endosymbiotic event, the very large diversity of plastids we observe today can only be explained by multiple layers of endosymbioses. That is, plastids were passed between distantly related eukaryotic lineages multiple times, essentially creating a phylogenetic imbroglio where plastids appear monophyletic but hosts are not. The burning question then is: how can we best fit plastid and host data into a comprehensive evolutionary framework? Focusing not only on the so-called complex plastids (the product of eukaryote-to-eukaryote endosymbioses) and the lineages that host them but also on the many related plastid-lacking lineages and orphan taxa, I discuss the emergence of new models of plastid evolution. These models generalize the notion of serial endosymbioses to explain the scattered distribution of plastids in the eukaryotic tree of life. As such, they make new testable predictions as to how complex algae are connected through endosymbiotic gene transfer, but testing this will require first to determine the real magnitude of this process.
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| 10. |
- Burki, Fabien, et al.
(author)
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The New Tree of Eukaryotes
- 2020
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In: Trends in Ecology & Evolution. - : ELSEVIER SCIENCE LONDON. - 0169-5347 .- 1872-8383. ; 35:1, s. 43-55
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Research review (peer-reviewed)abstract
- For 15 years, the eukaryote Tree of Life (eToL) has been divided into five to eight major groupings, known as 'supergroups'. However, the tree has been profoundly rearranged during this time. The new eToL results from the widespread application of phylogenomics and numerous discoveries of major lineages of eukaryotes, mostly free-living heterotrophic protists. The evidence that supports the tree has transitioned from a synthesis of molecular phylogenetics and biological characters to purely molecular phylogenetics. Most current supergroups lack defining morphological or cell-biological characteristics, making the supergroup label even more arbitrary than before. Going forward, the combination of traditional culturing with maturing culture-free approaches and phylogenomics should accelerate the process of completing and resolving the eToL at its deepest levels.
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