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- Jamy, Mahwash, et al.
(author)
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Global patterns and rates of habitat transitions across the eukaryotic tree of life
- 2022
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In: Nature Ecology & Evolution. - : Springer Nature. - 2397-334X. ; 6:10, s. 1458-1470
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Journal article (peer-reviewed)abstract
- The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.
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| 2. |
- Jamy, Mahwash, et al.
(author)
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Habitat, latitude, and the rate of molecular evolution in microbial eukaryotes
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Other publication (other academic/artistic)abstract
- Numerous studies over the years have found that molecular evolution does not progress in a constant, clock-like manner. Instead, evolutionary rates show complex patterns and can vary even between closely related species. Studying the underlying causes of these rate variations is important to improve our understanding of evolutionary processes. In this study, we investigate how majors habitat types (marine or terrestrial) and geography (latitude) can impact the rate of molecular evolution across the tree of eukaryotes, using long-read and short-read metabarcoding data placed in a phylogenetic framework. We did not find any systematic differences in the rate of evolution between marine and terrestrial species. However found a weak association between habitat colonization and increased rates of evolution. Evolutionary rates are expected to be higher in the tropics due to higher temperature, however we observed this pattern for only a few groups of marine protists. Several protist groups displayed no impact of latitude on rates of evolution, while some instead showed an inverse trend. These results cast doubt on the generality of the “kinetic energy hypothesis” which proposes a link between latitude/temperature and rates of molecular evolution.
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| 3. |
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| 4. |
- Vaulot, Daniel, et al.
(author)
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metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
- 2022
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In: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 22:8, s. 3188-3201
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Journal article (peer-reviewed)abstract
- In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities. The number of environmental data sets published has increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, are rarely available in a usable format. Clustered sequences are reported as operational taxonomic units (OTUs) with different similarity levels or more recently as amplicon sequence variants (ASVs). This hampers comparative studies between different environments and data sets, for example examining the biogeographical patterns of specific groups/species, as well analysing the genetic microdiversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. This database, called metaPR(2), contains 41 data sets corresponding to more than 4000 samples and 90,000 ASVs. The database, which is accessible through both a web-based interface () and an R package, should prove very useful to all researchers working on protist diversity in a variety of systems.
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