Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

@article{Szllsi2015GenomescalePA,
  title={Genome-scale phylogenetic analysis finds extensive gene transfer among fungi},
  author={Gergely J. Sz{\"o}llősi and Adri{\'a}n A. Dav{\'i}n and {\'E}ric Tannier and Vincent Daubin and Bastien Boussau},
  journal={Philosophical Transactions of the Royal Society B: Biological Sciences},
  year={2015},
  volume={370}
}
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes… 

Figures from this paper

A spectrum of verticality across genes
Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the
Horizontal Gene Transfer in Fungi
TLDR
Evidence of HGT is found heavily in parasitic and pathogenic fungi; both of these lifestyles rely on phagocytosis and assimilation of host parts and pieces, suggesting phagcytosis is implicated in DNA uptake mechanisms.
Extensive horizontal gene transfers between plant pathogenic fungi
TLDR
The results challenge the notion that HGT plays a minor role in the evolution of fungal lineages, and suggest that the expanding database of closely related eukaryotic genomes and the application of novel analytic methods will further underline the significant impact of foreign gene acquisition across the tree of life.
Gene transfers can date the Tree of Life
TLDR
It is shown that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life.
Gene transfers, like fossils, can date the Tree of Life
TLDR
New phylogenetic methods are used to reconstruct the history of thousands of gene families and it is demonstrated that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukaryotes.
The Sources of Phylogenetic Conflicts
TLDR
This chapter discusses compelling evidence for whole genome duplications in fish, as well as plants, and the role of horizontal transfer in the spread of antibiotic resistance and how these processes lead to phylogenetic conflict, and how they can be described by phylo-genetic models.
Universal markers support a long inter-domain branch between Archaea and Bacteria
TLDR
These analyses suggest that the apparent deep split between Archaea and Bacteria may be the result of accelerated evolution of ribosomal genes, and indicate that vertically-evolving marker genes across all functional categories support a major genetic divergence between the two primary domains of life.
Reconstruction of the evolutionary history of gene gains and losses since the last universal common ancestor.
TLDR
This is the most comprehensive genome-wide analysis of all events in gene evolutionary histories, constructed and analyzed over 10,000 gene family trees to reconstruct the gene content of ancestral genomes at an unprecedented scale, covering hundreds of genomes across all domains of life.
...
...

References

SHOWING 1-10 OF 49 REFERENCES
Gene transfer into the fungi
Computational inference of scenarios for alpha-proteobacterial genome evolution.
TLDR
This study uses computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree to reveal massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches separating intracellular bacteria of animals and humans.
Natural history and evolutionary principles of gene duplication in fungi
TLDR
This work develops a procedure that resolves the evolutionary history of all genes in a large group of species and applies it to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species.
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
TLDR
The results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record.
Lateral Gene Transfer from the Dead
TLDR
It is shown that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters and an algorithm is derived to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species.
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
TLDR
The results indicate that among 57,670 gene families distributed across 190 sequenced genomes, at least two-thirds and probably all, have been affected by LGT at some time in their evolutionary past and a component of common ancestry nonetheless remains detectable in gene distribution patterns.
The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives.
TLDR
It is suggested that the clade of cyanobacteria marked by cell differentiation diverged once between 2,450 and 2,100 Ma, providing an internal bacterial calibration point for studies of molecular evolution in early organisms.
Genome-scale coestimation of species and gene trees.
TLDR
A new probabilistic model is presented to jointly infer rooted species and gene trees for dozens of genomes and thousands of gene families and yields a more accurate picture of ancestral genomes than the trees available in the authoritative database Ensembl.
Modeling gene family evolution and reconciling phylogenetic discord.
TLDR
The approaches of increasing complexity aimed at extracting information on the pattern and process of gene family evolution from such datasets are discussed, and it is shown that the distribution of homologous gene family sizes in the genomes of the eukaryota, archaea, and bacteria exhibits remarkably similar shapes.
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
TLDR
This work has constructed robust phylogenies for fungi based on whole genome analysis that provide strong support for the classification of phyla, sub-phyla, classes and orders.
...
...