ORCID Profile
0000-0003-1072-0223
Current Organisation
University of Bristol
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Microbial ecology | Computational ecology and phylogenetics | Microbiology | Atmospheric composition chemistry and processes |
Publisher: Oxford University Press (OUP)
Date: 23-03-2023
DOI: 10.1093/GBE/EVAD051
Abstract: The origin of microbial mercury methylation has long been a mystery. Here, we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury-methylating gene, hgcAB, constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded by merB) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea.
Publisher: Oxford University Press (OUP)
Date: 25-09-2020
DOI: 10.1002/BJS.12050
Publisher: Cold Spring Harbor Laboratory
Date: 17-03-2023
DOI: 10.1101/2023.03.17.533068
Abstract: Species tree-aware phylogenetic methods model how gene trees are generated along the species tree by a series of evolutionary events, including the duplication, transfer and loss of genes. Over the past ten years these methods have emerged as a powerful tool for inferring and rooting gene and species trees, inferring ancestral gene repertoires, and studying the processes of gene and genome evolution. However, these methods are complex and can be more difficult to use than traditional phylogenetic approaches. Method development is rapid, and it can be difficult to decide between approaches and interpret results. Here, we review ALE and GeneRax, two popular packages for reconciling gene and species trees, explaining how they work, how results can be interpreted, and providing a tutorial for practical analysis. It was recently suggested that reconciliation-based estimates of duplication and transfer frequencies are unreliable. We evaluate this criticism and find that, provided parameters are estimated from the data rather than being fixed based on prior assumptions, reconciliation-based inferences are in good agreement with the literature, recovering variation in gene duplication and transfer frequencies across lineages consistent with the known biology of studied clades. For ex le, published datasets support the view that transfers greatly outnumber duplications in most prokaryotic lineages. We conclude by discussing some limitations of current models and prospects for future progress. Evolutionary trees provide a framework for understanding the history of life and organising bio ersity. In this review, we discuss some recent progress on statistical methods that allow us to combine information from many different genes within the framework of an overarching phylogenetic species tree. We review the advantages and uses of these methods and discuss case studies where they have been used to resolve deep branches within the tree of life. We conclude with the limitations of current methods and suggest how they might be overcome in the future.
Publisher: Cold Spring Harbor Laboratory
Date: 11-08-2023
DOI: 10.1101/2023.08.08.552427
Abstract: Most of life’s ersity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time. However, the co-evolution of life and the Earth system has left signatures of bacterial metabolism in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ∼2.33 billion years ago (Ga, (Poulton et al. 2021)), in which oxygenic photosynthesis and tectonism (Eguchi, Seales, and Dasgupta 2019) transformed Earth’s biosphere from dominantly anaerobic to aerobic. Here, we combine machine learning and phylogenetic reconciliation to infer ancestral transitions to aerobic lifestyles during bacterial evolution. Linking these transitions to the GOE provides new constraints to infer the timetree of Bacteria. We find that extant bacterial phyla are truly ancient, having radiated in the Archaean and the Proterozoic: the oldest include Bacillota (Firmicutes), which radiated 3.1-3.7 Ga, Cyanobacteria (3.3-3.5 Ga) and Patescibacteria (3-3.5 Ga). We show that most bacterial phyla were ancestrally anaerobic and that most transitions to an aerobic lifestyle post-dated the GOE. Our analyses trace oxygen production and consumption back to Cyanobacteria. From that starting point, horizontal transfer seeded aerobic lifestyles across bacterial ersity over hundreds of millions of years. Our analyses demonstrate that the ersification of aerobes proceeded in two waves corresponding to the GOE and to a second sustained rise in atmospheric O 2 at the dawn of the Palezoic (Krause et al. 2022).
Publisher: Springer Science and Business Media LLC
Date: 07-08-2020
DOI: 10.1038/S41467-020-17408-W
Abstract: The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life’s evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum ( Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported ‘DPANN’ clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts.
Publisher: Elsevier BV
Date: 05-2023
Publisher: Oxford University Press (OUP)
Date: 19-11-2013
DOI: 10.1093/GBE/EVT184
Publisher: Elsevier BV
Date: 08-2019
Publisher: Springer Science and Business Media LLC
Date: 04-01-2017
DOI: 10.1038/NCOMMS13932
Abstract: Microsporidians are obligate intracellular parasites that have minimized their genome content and sub-cellular structures by reductive evolution. Here, we demonstrate that cristae-deficient mitochondria (mitosomes) of Trachipleistophora hominis are the functional site of iron–sulfur cluster (ISC) assembly, which we suggest is the essential task of these organelles. Cell fractionation, fluorescence imaging and immunoelectron microscopy demonstrate that mitosomes contain a complete pathway for [2Fe–2S] cluster biosynthesis that we biochemically reconstituted using purified mitosomal ISC proteins. The T. hominis cytosolic iron–sulfur protein assembly (CIA) pathway includes the essential Cfd1–Nbp35 scaffold complex that assembles a [4Fe–4S] cluster as shown by spectroscopic methods in vitro . Phylogenetic analyses reveal that the ISC and CIA pathways are predominantly bacterial, but their cytosolic and nuclear target Fe/S proteins are mainly archaeal. This mixed evolutionary history of Fe/S-related proteins and pathways, and their strong conservation among highly reduced parasites, provides compelling evidence for the ancient chimeric ancestry of eukaryotes.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 07-05-2021
Abstract: The origin of the eubacteria and phylogenetic relationships between subgroups have been difficult to resolve. Applying a phylogenetic analysis and recent computational methods to the expanded ersity of bacterial sequences from metagenomic analyses, Coleman et al. infer the root of the eubacterial tree (see the Perspective by Katz). The root was determined without using the Archaea as an outgroup, to avoid the possibility of a false result due to long branch attraction. This method places the eubacterial root in the neighborhood of Fusobacteriota. Using this information, the authors reconstructed the eubacterial ancestor, identifying that this organism likely had a double-membrane cell envelope, flagellum-mediated motility, antiphage defense mechanisms, and erse metabolic pathways. Science , this issue p. eabe0511 see also p. 574
Publisher: Public Library of Science (PLoS)
Date: 25-10-2012
Publisher: Cold Spring Harbor Laboratory
Date: 05-03-2020
DOI: 10.1101/2020.03.05.976373
Abstract: The evolution and ersification of Archaea is central to the history of life on Earth. Cultivation-independent approaches have revealed the existence of at least ten archaeal lineages whose members have small cell and genome sizes and limited metabolic capabilities and together comprise the tentative DPANN archaea. However, the phylogenetic ersity of DPANN and the placement of the various lineages of this group in the archaeal tree remain debated. Here, we reconstructed additional metagenome assembled genomes (MAGs) of a thus far uncharacterized archaeal phylum-level lineage UAP2 ( Candidatus Undinarchaeota) affiliating with DPANN archaea. Comparative genome analyses revealed that members of the Undinarchaeota have small estimated genome sizes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of vitamins, amino acids and other metabolites. Phylogenomic analyses robustly recovered Undinarchaeota as a major independent lineage between two highly supported clans of DPANN: one clan comprising Micrarchaeota, Altiarchaeota and Diapherotrites, and another encompassing all other DPANN. Our analyses also suggest that DPANN archaea may have exchanged core genes with their hosts by horizontal gene transfer (HGT), adding to the difficulty of placing DPANN in the archaeal tree. Together, our findings provide crucial insights into the origins and evolution of DPANN archaea and their hosts.
Publisher: Cold Spring Harbor Laboratory
Date: 15-07-2020
DOI: 10.1101/2020.07.15.205187
Abstract: Bacteria are the most abundant and metabolically erse cellular lifeforms on Earth. A rooted bacterial phylogeny provides a framework to interpret this ersity and to understand the nature of early life. Inferring the position of the bacterial root is complicated by incomplete taxon s ling and the long branch to the archaeal outgroup. To circumvent these limitations, we model bacterial genome evolution at the level of gene duplication, transfer and loss events, allowing outgroup-free inference of the root 1 . We infer a rooted bacterial tree on which 68% of gene transmission events are vertical. Our analyses reveal a basal split between Terrabacteria and Gracilicutes, which together encompass almost all known bacterial ersity. However, the position of one phylum, Fusobacteriota, could not be resolved in relation to these two major clades. In contrast to recent proposals, our analyses strongly reject a root between the Candidate Phyla Radiation (CPR) and all other Bacteria. Instead, we find that the CPR is a sister lineage to the Chloroflexota within the Terrabacteria. We predict that the last bacterial common ancestor was a free-living flagellated, rod-shaped cell featuring a double membrane with a lipopolysaccharide outer layer, a Type III CRISPR-Cas system, Type IV pili, and the ability to sense and respond via chemotaxis.
Publisher: Portland Press Ltd.
Date: 14-11-2018
DOI: 10.1042/ETLS20180021
Publisher: The Company of Biologists
Date: 15-02-2018
DOI: 10.1242/BIO.032524
Abstract: The concept of symbiosis – defined in 1879 by de Bary as ‘the living together of unlike organisms’ – has a rich and convoluted history in biology. In part, because it questioned the concept of the in idual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, erse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for ex le, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists’ workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.
Publisher: Public Library of Science (PLoS)
Date: 13-04-2022
DOI: 10.1371/JOURNAL.PBIO.3001601
Abstract: Coat complexes coordinate cargo recognition through cargo adaptors with biogenesis of transport carriers during integral membrane protein trafficking. Here, we combine biochemical, structural, and cellular analyses to establish the mechanistic basis through which SNX27–Retromer, a major endosomal cargo adaptor, couples to the membrane remodeling endosomal SNX-BAR sorting complex for promoting exit 1 (ESCPE-1). In showing that the SNX27 FERM (4.1/ezrin/radixin/moesin) domain directly binds acidic-Asp-Leu-Phe (aDLF) motifs in the SNX1/SNX2 subunits of ESCPE-1, we propose a handover model where SNX27–Retromer captured cargo proteins are transferred into ESCPE-1 transport carriers to promote endosome-to-plasma membrane recycling. By revealing that assembly of the SNX27:Retromer:ESCPE-1 coat evolved in a stepwise manner during early metazoan evolution, likely reflecting the increasing complexity of endosome-to-plasma membrane recycling from the ancestral opisthokont to modern animals, we provide further evidence of the functional ersification of yeast pentameric Retromer in the recycling of hundreds of integral membrane proteins in metazoans.
Publisher: Public Library of Science (PLoS)
Date: 16-06-2011
Publisher: Cold Spring Harbor Laboratory
Date: 24-11-2022
DOI: 10.1101/2022.11.21.517362
Abstract: The origin of microbial mercury methylation has long been a mystery. Here we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury methylating gene, hgcAB , constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg + ) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg + -detoxifying alkylmercury lyase (encoded by merB ) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea. Neurotoxic methylmercury (MeHg + (aq) ) is synthesized from Hg II (aq) in the environment by microorganisms possessing the gene pair hgcAB . Our phylogenetic analyses elucidate the origin and evolution of the hgc operon, and support a hypothesis that mercury methylation evolved as an antimicrobial production mechanism, possibly from competition for limited resources on the early Earth. We infer from our analyses that hgc has been primarily vertically inherited in Bacteria and Archaea, with extensive parallel loss, and note that few taxa possessing hgc also possess the gene encoding for MeHg + demethylation, merB . Our findings support the interpretation that merB evolved as a defense mechanism against the evolution of microbial Hg II (aq) methylation.
Publisher: Oxford University Press (OUP)
Date: 07-2023
DOI: 10.1093/GBE/EVAD134
Abstract: ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root in Bacteria—where there is less certainty about the root position—ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.
Publisher: Public Library of Science (PLoS)
Date: 04-12-2014
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 2023
End Date: 12-2025
Amount: $374,079.00
Funder: Australian Research Council
View Funded Activity