Corrigendum to: Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition

Arroyo, Alicia S.; Iannes, Romain; Bapteste, Éric; Ruiz‐Trillo, Iñaki

doi:10.1093/gbe/evab140

Cited by 3 publications

(3 citation statements)

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“…Most likely, there are additional unicellular lineages that are closely related to animals. In particular, analyses of environmental DNA from marine and freshwater samples have shown that we are missing not only many species, which is expected, but also several higher-rank groups, some of which could even be at the same taxon level as choanoflagellates or ichthyosporeans (4,5,16). Even more importantly, these studies did not specifically target unicellular holozoans, but rather eukaryotes in general, so the possibility of discovering additional lineages if a targeted survey were to be conducted is very high.…”

Section: Environmental Dna Analyses Reveal Far Too Many Unknowns Amon...mentioning

confidence: 89%

The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event

Ruiz‐Trillo

Kin

Casacuberta

2023

Annu. Rev. Microbiol.

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The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Section: Environmental Dna Analyses Reveal Far Too Many Unknowns Amon...mentioning

confidence: 89%

The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event

Ruiz‐Trillo

Kin

Casacuberta

2023

Annu. Rev. Microbiol.

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“…The concept of closeness centrality has been utilised to identify which metabolites are particularly important in genome-based, large-scale metabolic networks [86], contrast unicellular and multicellular animals [87,88], rank pathways [89][90][91], and gain insight into the evolution of metabolic organisation [35,92]. The process of evolution has resulted in an increase in the distance between different routes, which has led to a decrease in the closeness and centrality of different components.…”

Section: Maximal Clique Centrality (Mcc)mentioning

confidence: 99%

A Mini Review of Node Centrality Metrics in Biological Networks

Wang

Zheng

2022

IJNDI

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Survey/review study A Mini Review of Node Centrality Metrics in Biological Networks Mengyuan Wang 1,2, Haiying Wang 1, and Huiru Zheng 1,* 1 School of Computing, Ulster University, Belfast, BT15 1ED, United Kingdom 2 Scotland’s Rural College, Edinburgh, EH25 9RG, United Kingdom * Correspondence: h.zheng@ulster.ac.uk Received: 31 October 2022 Accepted: 21 November 2022 Published: 22 December 2022 Abstract: The diversity of nodes in a complex network causes each node to have varying significance, and the important nodes often have a significant impact on the structure and function of the network. Although the interpretation of the results of biological networks must always depend on the topological study of nodes, there is presently no consensus on how to use these metrics, and most network analyses always result in a basic interpretation of a limited number of metrics. To thoroughly comprehend biological networks, it is necessary to consistently understand the notion of node centrality. Therefore, for 10 typical nodal metrics in biological networks, the study first assesses their current applications, advantages, disadvantages as well as potential applications. Then, a review of previous studies is provided, and suggestions are made correspondingly for the purpose of improving biological topology algorithms. Finally, the following recommendations are made in this study: (1) a comprehensive and accurate assessment of node centrality necessitates the use of multiple metrics, including both the target node and its surroundings, and density of maximum neighbourhood component(DMNC) can be used as a complement to other node centrality metrics; (2) different centrality metrics can be applied to identify nodes with different functions, which in this study are mapped as modular surroundings, bridging roles, and susceptibility; and (3) the following groups of node centrality can often be verified against each other, including degree and maximum neighbourhood component (MNC), eccentricity, closeness and radiality; stress and betweenness.

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“…Co-occurrence networks, for instance, can help assessing ecological roles of unknown taxa [33]. Sequence similarity networks, wherein pairs of primary sequences are connected according to set similarity criteria, can also be employed to compare sequences from cultured and uncultured organisms [34,35]. In 2012, Lynch et al used sequence similarity networks to identify several candidate new lineages from environmental 16S rRNA [36].…”

Section: Introductionmentioning

confidence: 99%

New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean

Sussfeld,

Lannes,

Corel

et al. 2024

Preprint

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Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating microbial adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the tree of life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters, including at relatively lenient clustering thresholds. Here, we used an iterative network-based approach to probe a dataset of 40 million ORFs, predicted in marine environments. We assessed the environmental diversity of a selection of 53 gene families as old as cellular life, broadly distributed across the Tree of Life. About half of them harboured clusters of environmental homologs that diverged significantly from the known diversity of published complete genomes, with representatives distributed across all the ocean. Network analyses also enabled the detection of environmental clades with new structural variants of essential genes (SMC), divergent polymerase subunits forming deep branching clades in the polymerase tree, and potentially deep taxonomic groups at the basis of Archaea or Bacteria, from ultra-small microorganisms distinct from CPR and DPANN. These diverse results provide a strong proof of concept for the capabilities of sequence network approaches to make better sense of microbial dark matter across taxonomical scales. Still, further methodological developments appear warranted in order to better comprehend the most divergent members of the oceanic microbial dark matter.

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Corrigendum to: Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition

Cited by 3 publications

References 0 publications

The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event

The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event

A Mini Review of Node Centrality Metrics in Biological Networks

New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean

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