Phylogenetic reconciliation

Menet, Hugo; Daubin, Vincent; Tannier, Éric

doi:10.1371/journal.pcbi.1010621

Cited by 12 publications

(2 citation statements)

References 180 publications

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“…Although most attention has been focused on reconciliation of gene and species trees, phylogenetic reconciliation has the potential to be applied to other systems with similar hierarchical relationships [ 8 ]. Of potential interest to microbial ecologists is the use of phylogenetic reconciliation to model host-symbiont coevolution and the evolution of microbiome composition over time, where the symbionts are the “genes” and the host is the “species.” The approach could be used to determine the extent and timescale of host-symbiont coevolution and to identify host (or symbiont) switching events [ 99 , 100 ].…”

Section: Modelling Microbial Evolutionmentioning

confidence: 99%

“…As with any kind of data analysis, the accuracy of phylogenetic reconciliation depends on the algorithms used and the assumptions they make about the processes of evolution [ 7 ]. There has been substantial progress in method development in recent years [ 8 ], including the development of methods that can accommodate uncertainty in the evolutionary history of single genes [ 9–11 ], incomplete lineage sorting [ 12 ], and that allow the inferred rates of gene duplication, transfer, and loss (DTL) to vary across the species tree [ 4 ], resulting in more sophisticated software packages for performing these analyses. Here, we first review how reconciliation methods work and argue that they provide a natural framework for modelling microbial genome evolution.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution

Williams,

Davin,

Szánthó

et al. 2024

The ISME Journal

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In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host–microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.

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Section: Modelling Microbial Evolutionmentioning

confidence: 99%