Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method

Bremer, Nico; Knopp, Michael; Martin, William; Tria, Fernando D. K.

doi:10.3390/life12070995

Cited by 9 publications

(46 citation statements)

References 49 publications

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“…Based on this understanding, we summarise what published analyses have concluded about variation in the processes of molecular evolution across the tree of life. We also clarify a number of potential misconceptions about these methods and their results in the recent critiques (Tria & Martin 2021; Bremer et al 2022), and show that reconciliation-based inferences about frequencies of duplication, transfer and loss are in good agreement with previous results using other methods. Finally, we provide a practical guide for researchers who wish to use reconciliation tools to perform phylogenomic and comparative genomic analyses, review current limitations and suggest future directions for addressing them.…”

Section: Introductionsupporting

confidence: 69%

“…In their recent critique of ALE, (Bremer et al 2022) suggested that estimated rates of duplication and transfer were biologically unrealistic for two datasets from different domains of life because they failed to capture the expected difference in the dynamics of genome evolution between Bacteria (Coleman et al 2021) and eukaryotes (Bremer et al 2022). To evaluate these claims, we summarised the ALE output from the two datasets (Figure 3).…”

Section: Do Prior Assumptions Bias the Estimation Of Model Parameters...mentioning

confidence: 99%

“…As a result, gene families that experience very few DTL events have very limited power to identify the root of the species tree, because a perfectly congruent gene tree is equally consistent with all species tree root positions. This explains why the analysis of the single-copy marker genes from the fungi-metazoa dataset did not distinguish the root of the tree in Bremer et al (2022)'s experiments; these genes have experienced no inferred duplications and very few inferred transfers or losses (Table 1).…”

Section: The Nature Of the Root Signal In Reconciliation Analysesmentioning

confidence: 99%

“…Tria and Martin (2021) criticised the rates of gene duplication and transfer (and in particular, the ratios of these rates) inferred using ALE because they were inconsistent with the large excess of gene transfers over duplications in prokaryotic genomes frequently observed in previous analyses (Lerat et al 2005; Treangen & Rocha 2011; Tria & Martin 2021). In a subsequent paper (Bremer et al 2022), these and other authors argued that transfer and duplication rate ratios in ALE analyses were unrealistic, and that these biases affect the inference of rooted species trees using the ALE model.…”

Section: Introductionmentioning

confidence: 99%

“…for example, the parsimony method RANGER-DTL(Bansal et al 2018)); however, all of the analyses criticised inTria and Martin (2021) andBremer et al (2022) were performed using ALE, which directly estimates these values from the data. Bremer et al (2022) further suggested that the default equal initial values for and -that are required by the Bio++ implementation (Guéguen et al 2013) of the standard Nelder-Mead optimization algorithm used in ALE for maximising the likelihood -have an undue influence on the optimised values, although they did not provide any evidence to support the claim.…”

mentioning

confidence: 99%

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The power and limitations of species tree-aware phylogenetics

Williams

Davín

Morel

et al. 2023

Preprint

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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 example, 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.

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Section: Introductionsupporting

confidence: 69%

Section: Do Prior Assumptions Bias the Estimation Of Model Parameters...mentioning

confidence: 99%

Section: The Nature Of the Root Signal In Reconciliation Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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The power and limitations of species tree-aware phylogenetics

Williams

Davín

Morel

et al. 2023

Preprint

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Illuminating the coevolution of photosynthesis and Bacteria

Nishihara,

Tsukatani,

Azai

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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Life harnessing light energy transformed the relationship between biology and Earth—bringing a massive flux of organic carbon and oxidants to Earth’s surface that gave way to today’s organotrophy- and respiration-dominated biosphere. However, our understanding of how life drove this transition has largely relied on the geological record; much remains unresolved due to the complexity and paucity of the genetic record tied to photosynthesis. Here, through holistic phylogenetic comparison of the bacterial domain and all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence between three independent biological systems—bacteria, (bacterio)chlorophyll-mediated light metabolism (chlorophototrophy), and carbon fixation—and uncover their intertwined history. Our analyses uniformly mapped progenitors of extant light-metabolizing machinery (reaction centers, [bacterio]chlorophyll synthases, and magnesium-chelatases) and enzymes facilitating the Calvin–Benson–Bassham cycle (form I RuBisCO and phosphoribulokinase) to the same ancient Terrabacteria organism near the base of the bacterial domain. These phylogenies consistently showed that extant phototrophs ultimately derived light metabolism from this bacterium, the last phototroph common ancestor (LPCA). LPCA was a non-oxygen-generating (anoxygenic) phototroph that already possessed carbon fixation and two reaction centers, a type I analogous to extant forms and a primitive type II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution of chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, the rise of oxygen-generating chlorophototrophy in one descendant branch near the Great Oxidation Event, and subsequent emergence of Cyanobacteria. These collectively unveil a detailed view of the coevolution of light metabolism and Bacteria having clear congruence with the geological record.

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Phylogenomic Testing of Root Hypotheses

Tria

Landan

Picazo

2023

Genome Biology and Evolution

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The determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully resolved species tree. From a theoretical perspective, however, inference of the LCA amounts to the reconstruction of just one branch - the root branch - of the true species tree, and should therefore be a much easier task than the full resolution of the species tree. Discarding the reliance on a hypothesised species tree and its rooting leads us to re-evaluate what phylogenetic signal is directly relevant to LCA inference, and to recast the task as that of sampling the total evidence from all gene families at the genomic scope. Here we reformulate LCA and root inference in the framework of statistical hypothesis testing and outline an analytical procedure to formally test competing a-priori LCA hypotheses and to infer confidence sets for the earliest speciation events in the history of a group of species. Applying our methods to two demonstrative datasets we show that our inference of the opisthokonta LCA is well in agreement with the common knowledge. Inference of the proteobacteria LCA shows that it is most closely related to modern Epsilonproteobacteria, raising the possibility that it may have been characterized by a chemolithoautotrophic and anaerobic life-style. Our inference is based on data comprising between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching LCA inference within a statistical framework renders the phylogenomic inference powerful and robust.

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Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method

Cited by 9 publications

References 49 publications

The power and limitations of species tree-aware phylogenetics

The power and limitations of species tree-aware phylogenetics

Illuminating the coevolution of photosynthesis and Bacteria

Phylogenomic Testing of Root Hypotheses

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