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Article ; Online: On the Comparison of Incompatibility of Split Systems Across Different Numbers of Taxa.

Hendriksen, Michael / Kapust, Nils

2021 Volume 83, Issue 7, Page(s) 78

Abstract: We consider the problem of the minimum number of phylogenetic trees it would take to display all splits in a given set, a problem related to k-compatibility. A set of trees that displays every single possible split is termed a universal tree set. In this ...

Abstract	We consider the problem of the minimum number of phylogenetic trees it would take to display all splits in a given set, a problem related to k-compatibility. A set of trees that displays every single possible split is termed a universal tree set. In this note, we find the universal incompatibility U(n), the minimal size of a universal tree set for n taxa. By normalising incompatibility using U(n), one can then compare incompatibility of split systems across different numbers of taxa. We demonstrate this application by comparing two SplitsTree networks derived from archaeal genomes, with different numbers of taxa.
MeSH term(s)	Mathematical Concepts ; Models, Genetic ; Phylogeny
Language	English
Publishing date	2021-05-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	184905-0
ISSN	1522-9602 ; 0007-4985 ; 0092-8240
ISSN (online)	1522-9602
ISSN	0007-4985 ; 0092-8240
DOI	10.1007/s11538-021-00911-6
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Article: The origin and distribution of the main oxygen sensing mechanism across metazoans.

Song, Bing / Modjewski, Luca David / Kapust, Nils / Mizrahi, Itzhak / Martin, William F

Frontiers in physiology

2022 Volume 13, Page(s) 977391

Abstract: Oxygen sensing mechanisms are essential for metazoans, their origin and evolution in the context of oxygen in Earth history are of interest. To trace the evolution of a main oxygen sensing mechanism among metazoans, the hypoxia induced factor, HIF, we ... ...

Abstract	Oxygen sensing mechanisms are essential for metazoans, their origin and evolution in the context of oxygen in Earth history are of interest. To trace the evolution of a main oxygen sensing mechanism among metazoans, the hypoxia induced factor, HIF, we investigated the phylogenetic distribution and phylogeny of 11 of its components across 566 eukaryote genomes. The HIF based oxygen sensing machinery in eukaryotes can be traced as far back as 800 million years (Ma) ago, likely to the last metazoan common ancestor (LMCA), and arose at a time when the atmospheric oxygen content corresponded roughly to the Pasteur point, or roughly 1% of present atmospheric level (PAL). By the time of the Cambrian explosion (541-485 Ma) as oxygen levels started to approach those of the modern atmosphere, the HIF system with its key components HIF1α, HIF1β, PHD1, PHD4, FIH and VHL was well established across metazoan lineages. HIF1α is more widely distributed and therefore may have evolved earlier than HIF2α and HIF3α, and HIF1β and is more widely distributed than HIF2β in invertebrates. PHD1, PHD4, FIH, and VHL appear in all 13 metazoan phyla. The O
Language	English
Publishing date	2022-10-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2022.977391
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Book ; Online: On the comparison of incompatibility of split systems across different numbers of taxa

Hendriksen, Michael / Kapust, Nils

2020

Abstract: The concept of $k$-compatibility measures how many phylogenetic trees it would take to display all splits in a given set. A set of trees that display every single possible split is termed a \textit{universal tree set}. In this note, we find $A(n)$, the ... ...

Abstract	The concept of $k$-compatibility measures how many phylogenetic trees it would take to display all splits in a given set. A set of trees that display every single possible split is termed a \textit{universal tree set}. In this note, we find $A(n)$, the minimal size of a universal tree set for $n$ taxa. By normalising the $k$-compatibility using $A(n)$, one can then compare incompatibility of split systems across different taxa sizes. We demonstrate this application by comparing two SplitsTree networks of different sizes derived from archaeal genomes. Comment: 9 pages, 2 figures. Updated to make writing and proofs clearer, some additional information included
Keywords	Quantitative Biology - Populations and Evolution ; Mathematics - Combinatorics ; 92B10
Publishing date	2020-03-31
Publishing country	us
Document type	Book ; Online
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Article ; Online: Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans.

Moraïs, Sarah / Winkler, Sarah / Zorea, Alvah / Levin, Liron / Nagies, Falk S P / Kapust, Nils / Lamed, Eva / Artan-Furman, Avital / Bolam, David N / Yadav, Madhav P / Bayer, Edward A / Martin, William F / Mizrahi, Itzhak

Science (New York, N.Y.)

2024 Volume 383, Issue 6688, Page(s) eadj9223

Abstract: Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota ... ...

Abstract	Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.
MeSH term(s)	Humans ; Cellulose/metabolism ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Microbiome/physiology ; Ruminococcus/classification ; Ruminococcus/enzymology ; Ruminococcus/genetics ; Dietary Fiber/metabolism ; Phylogeny ; Industrial Development
Chemical Substances	Cellulose (9004-34-6) ; Dietary Fiber
Language	English
Publishing date	2024-03-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.adj9223
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Article ; Online: Elusive data underlying debate at the prokaryote-eukaryote divide.

Gerlitz, Marie / Knopp, Michael / Kapust, Nils / Xavier, Joana C / Martin, William F

Biology direct

2018 Volume 13, Issue 1, Page(s) 21

Abstract: Background: The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote ... ...

Abstract	Background: The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature. Results: We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure. Conclusion: The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution. Reviewers: This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.
MeSH term(s)	Biological Evolution ; Energy Metabolism ; Eukaryotic Cells/physiology ; Mitochondria/metabolism ; Prokaryotic Cells/physiology
Language	English
Publishing date	2018-10-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1745-6150
ISSN (online)	1745-6150
DOI	10.1186/s13062-018-0221-x
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Article ; Online: Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity.

Tria, Fernando D K / Brueckner, Julia / Skejo, Josip / Xavier, Joana C / Kapust, Nils / Knopp, Michael / Wimmer, Jessica L E / Nagies, Falk S P / Zimorski, Verena / Gould, Sven B / Garg, Sriram G / Martin, William F

Genome biology and evolution

2021 Volume 13, Issue 5

Abstract: The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of ... ...

Abstract	The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of eukaryote complexity remain debated. Here, we report evidence from gene duplications in LECA indicating an early origin of mitochondria. Among 163,545 duplications in 24,571 gene trees spanning 150 sequenced eukaryotic genomes, we identify 713 gene duplication events that occurred in LECA. LECA's bacterial-derived genes include numerous mitochondrial functions and were duplicated significantly more often than archaeal-derived and eukaryote-specific genes. The surplus of bacterial-derived duplications in LECA most likely reflects the serial copying of genes from the mitochondrial endosymbiont to the archaeal host's chromosomes. Clustering, phylogenies and likelihood ratio tests for 22.4 million genes from 5,655 prokaryotic and 150 eukaryotic genomes reveal no evidence for lineage-specific gene acquisitions in eukaryotes, except from the plastid in the plant lineage. That finding, and the functions of bacterial genes duplicated in LECA, suggests that the bacterial genes in eukaryotes are acquisitions from the mitochondrion, followed by vertical gene evolution and differential loss across eukaryotic lineages, flanked by concomitant lateral gene transfer among prokaryotes. Overall, the data indicate that recurrent gene transfer via the copying of genes from a resident mitochondrial endosymbiont to archaeal host chromosomes preceded the onset of eukaryotic cellular complexity, favoring mitochondria-early over mitochondria-late hypotheses for eukaryote origin.
MeSH term(s)	Biological Evolution ; Eukaryota/genetics ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Mitochondria/genetics
Language	English
Publishing date	2021-03-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evab055
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Article ; Online: Elusive data underlying debate at the prokaryote-eukaryote divide

Marie Gerlitz / Michael Knopp / Nils Kapust / Joana C. Xavier / William F. Martin

Biology Direct, Vol 13, Iss 1, Pp 1-

2018 Volume 12

Abstract: Abstract Background The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for ... ...

Abstract	Abstract Background The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature. Results We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure. Conclusion The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in ...
Keywords	Eukaryogenesis ; Mitochondria ; Ribosomes ; Bioenergetics ; Major evolutionary transitions ; Biology (General) ; QH301-705.5
Subject code	501
Language	English
Publishing date	2018-10-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea.

Garg, Sriram G / Kapust, Nils / Lin, Weili / Knopp, Michael / Tria, Fernando D K / Nelson-Sathi, Shijulal / Gould, Sven B / Fan, Lu / Zhu, Ruixin / Zhang, Chuanlun / Martin, William F

Genome biology and evolution

2020 Volume 13, Issue 1

Abstract: Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages ... ...

Abstract	Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.
MeSH term(s)	Archaea/genetics ; Ecosystem ; Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; Genome, Archaeal ; Genomics ; Metagenome ; Metagenomics ; Phylogeny ; Ribosomal Proteins/classification ; Ribosomal Proteins/genetics
Chemical Substances	Ribosomal Proteins
Language	English
Publishing date	2020-11-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evaa238
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Article ; Online: Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication.

Kapust, Nils / Nelson-Sathi, Shijulal / Schönfeld, Barbara / Hazkani-Covo, Einat / Bryant, David / Lockhart, Peter J / Röttger, Mayo / Xavier, Joana C / Martin, William F

Genome biology and evolution

2018 Volume 10, Issue 5, Page(s) 1198–1209

Abstract: In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from ... ...

Abstract	In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.
MeSH term(s)	Archaea/genetics ; Chloroplast Proteins/genetics ; Computational Biology/standards ; Eukaryota/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plastid ; Genomics ; Models, Genetic ; Phylogeny ; Plastids/classification ; Plastids/genetics ; Software ; Symbiosis/genetics ; Validation Studies as Topic
Chemical Substances	Chloroplast Proteins
Language	English
Publishing date	2018-05-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Technical Report
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evy080
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