Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention

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Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention. / Johnston, Iain G.; Williams, Ben P.

In: Cell Systems, Vol. 2, No. 2, 24.02.2016, p. 101-111.

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@article{cf01f8fa75cc44abb7e44a6575f7943c,
title = "Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention",
abstract = "Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species.",
author = "Johnston, {Iain G.} and Williams, {Ben P.}",
year = "2016",
month = feb,
day = "24",
doi = "10.1016/j.cels.2016.01.013",
language = "English",
volume = "2",
pages = "101--111",
journal = "Cell Systems",
issn = "2405-4712",
publisher = "Elsevier",
number = "2",

}

RIS

TY - JOUR

T1 - Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention

AU - Johnston, Iain G.

AU - Williams, Ben P.

PY - 2016/2/24

Y1 - 2016/2/24

N2 - Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species.

AB - Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species.

UR - http://www.scopus.com/inward/record.url?scp=84959573074&partnerID=8YFLogxK

U2 - 10.1016/j.cels.2016.01.013

DO - 10.1016/j.cels.2016.01.013

M3 - Article

AN - SCOPUS:84959573074

VL - 2

SP - 101

EP - 111

JO - Cell Systems

JF - Cell Systems

SN - 2405-4712

IS - 2

ER -