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Pervasive selection biases inferences of the species tree
[article]
2020
bioRxiv
pre-print
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Despite the importance of natural selection in species' evolutionary history, phylogenetic methods that take into account population-level processes ignore selection. Assuming neutrality is often based on the idea that selection occurs at a minority of loci in the genome and is unlikely to significantly compromise phylogenetic inferences. However, selection might behave more pervasively, as it the case of nearly neutral evolving mutations. Genome-wide processes like GC-bias and some of the
doi:10.1101/2020.07.30.228965
fatcat:qua3bxnygvdc5aap77fea33wem
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... tion segregating at the coding regions are known to evolve in the nearly neutral range. As we are now using genome-wide data to estimate species tree, it is just natural to ask whether weak, but pervasive, selection is likely to blur species tree inferences. Here, we employed a polymorphism-aware phylogenetic model, specially tailored for measuring signatures of nucleotide usage biases, to test the impact of nearly neutrally in the substitution process. Analyses with simulated data indicate that while the inferred relationships among species are not significantly compromised, the genetic distances are systematically underestimated, with the deeper nodes suffering more than the younger ones. Such biases have implications for molecular dating. We found signatures of GC-bias considerably affecting the estimated divergence times (up to 21%) of worldwide fruit fly populations. Our findings call for the need to account for nearly neutral forces (or any other form of pervasive selection) when quantifying divergence or dating species evolution.
The inference of gene trees with species trees
[article]
2013
arXiv
pre-print
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On one hand, Boussau et al. programming, but without considering dated gene trees. This allowed them to avoid using a model of rate evolution. ...
As such searches can be computationally intensive, SPRs are sometimes bounded [Boussau et al., 20 2013] , or rearrangements are directed [Szöllősi et al., 2012] . ...
arXiv:1311.0651v1
fatcat:nwhpj4yuojcwdinu5jcxjhsiie
Accurate detection of convergent amino-acid evolution with PCOC
[article]
2018
bioRxiv
pre-print
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We used bppml (Dutheil and Boussau, 2008) to measure the likelihood of each model. ...
associated to each branch, with rate heterogeneity across sites according to a Gamma distribution discretized in 4 classes (Yang, 1994) with the α parameter set to 1.0, using bppseqgen (Dutheil and Boussau ...
doi:10.1101/247296
fatcat:xl4szq4kmralzkczbbx4bn63ma
Relative time constraints improve molecular dating
[article]
2020
biorxiv/medrxiv
pre-print
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Scripts are available at https://github.com/Boussau/DatingWithConsAndCal. ...
The script is available at https://github.com/Boussau/DatingWithConsAndCal/blob/master/Scripts/mcmc_JC.Rev. ...
Data availability Scripts and data used to run the simulation analyses are available at https://github.com/Boussau/DatingWithConsAndCal Data for the empirical data analysis has been deposited at: https ...
doi:10.1101/2020.10.17.343889
fatcat:xlsebfnnqnhxtff6x6pg4lgapm
Probabilistic Graphical Model Representation in Phylogenetics
[article]
2013
arXiv
pre-print
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using site-specific rate-multipliers , branch-specific rate-multipliers ), branch-specific substitution rate matrices (Yang and Roberts 1995; Galtier and Gouy 1998) and site-specific tree topologies (Boussau ...
Hence, belief propagation can be used in various other examples such as a mixture over the rates of positive selection (Yang and Nielsen 2002; Huelsenbeck and Dyer 2004) , mixture over tree topologies (Boussau ...
arXiv:1312.2386v1
fatcat:7retp2em7fg33b37zlruxrb4ua
Bayesian investigation of SARS-CoV-2-related mortality in France
[article]
2020
biorxiv/medrxiv
pre-print
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fr/boussau/corona_french_regions ; an archive of the code state at the time of publication
m is the Peer Community In Mathematical and Computational Biology
4 of 28
. ...
doi:10.1101/2020.06.09.20126862
fatcat:c6fko4v4wbellbukig3hspfvvq
Drift and Genome Complexity Revisited
2011
PLoS Genetics
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Relative time constraints improve molecular dating
2021
Systematic Biology
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Scripts are available at 12 https://github.com/Boussau/DatingWithConsAndCal. ...
with 102 taxa, calibrated nodes and node order constraints.
).Python code using the ete3 library (Huerta-Cepas, Serra, and Bork 2016) and RevBayes code to simulate sequences and https://github.com/Boussau ...
doi:10.1093/sysbio/syab084
pmid:34668564
fatcat:vaqukambwrcavlntg3mpg6b6si
Detecting convergent adaptive amino acid evolution: Supplementary material
[article]
2019
bioRxiv
pre-print
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In evolutionary genomics, researchers have taken an interest in identifying in the genomes substitutions that subtend convergent phenotypic adaptations. This is a difficult question to address, because genomes contain billions of sites, many of which have substituted in the lineages where the adaptations took place, and yet are not linked to them. Those extra substitutions may be linked to other adaptations, may be neutral, or may be linked to mutational biases. Furthermore, one can think of
doi:10.1101/513010
fatcat:4j7fusbytzbzpi4kdfnayi6p6u
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... ious ways of defining substitutions of interest, and various methods that match those definitions have been used, resulting in different sets of candidate substitutions. In this manuscript we first clarify how adaptation to convergent phenotypic evolution can manifest itself in coding sequences. Second, we review methods that have been proposed to detect convergent adaptive evolution in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes, including in the presence of a confounding factor.
Efficient Exploration of the Space of Reconciled Gene Trees
[article]
2013
arXiv
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and Daubin, 2010; Boussau et al., 2012) . ...
Joint inference of species and gene trees offers a path toward surmounting this obstacle (Boussau and Daubin, 2010; Boussau et al., 2012; . ...
arXiv:1306.2167v1
fatcat:a6gqpyr2urhjvn6nirevk3k7rm
Bayesian investigation of SARS-CoV-2-related mortality in France
2022
Peer Community Journal
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The code used for the experiments is available at https://gitlab.in2p3.fr/boussau/corona_ french_regions
Results We first investigate whether model 1 can capture the major trends of the epidemic in the ...
doi:10.24072/pcjournal.84
fatcat:x6ydhlbalnbezgcc5ikvz2yki4
CAARS: comparative assembly and annotation of RNA-Seq data
2018
Bioinformatics
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Quality of the trees can be improved by using reconstruction methods that use the information provided by the species tree (Boussau et al., 2013; Ullah et al., 2015) . ...
Then, accurate gene trees are inferred using a phylogenetic pipeline that uses the information coming from both the alignments and the species tree (Boussau et al., 2013) and identifies events of gene ...
doi:10.1093/bioinformatics/bty903
pmid:30452539
pmcid:PMC6596894
fatcat:6zgu2kwjpzf7jncddtotwlcwy4
Gene transfers, like fossils, can date the Tree of Life
[article]
2017
bioRxiv
pre-print
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Biodiversity has always been predominantly microbial and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here we show that patterns of lateral gene transfer deduced from the analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use new phylogenetic methods to reconstruct the history of thousands of gene families
doi:10.1101/193813
fatcat:tpofgtu6erf5ppmit7qw4urche
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... demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukaryotes. An inspection of discrepancies between transfers and clocks and a comparison with mammal fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.
The Inference of Gene Trees with Species Trees
2014
Systematic Biology
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Figure reprinted with permission from Boussau et al. (2013) . ...
As such searches can be computationally intensive, SPRs are sometimes bounded (Boussau et al. 2013) , or rearrangements are directed . ...
doi:10.1093/sysbio/syu048
pmid:25070970
pmcid:PMC4265139
fatcat:lsfkomvpfzdkff6gec46y34d6a
Parallel adaptations to high temperatures in the Archaean eon
2008
Nature
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Because fossils from the time when cellular life originated and diversified are scant and difficult to interpret 1 , alternative means to investigate the ecology of the Last Universal Common Ancestor (LUCA) and of the ancestors of the three domains of life are of great scientific value. It was recently recognized that footprints of the effect of temperature on ancestral organisms could be uncovered in extant genomes 2-4 . Accordingly, analyses of resurrected proteins predicted that the
doi:10.1038/nature07393
pmid:19037246
fatcat:f3pzhvme5fewrbkc6gn6cn53fa
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... ancestor was thermophilic and that Bacteria subsequently adapted to lower temperatures 3,4 . Since the archaeal ancestor is also thought to have been thermophilic 5 , LUCA was parsimoniously inferred as thermophilic too. However, an analysis of ribosomal RNAs supported the hypothesis of a non-hyperthermophilic LUCA 2 . Here we show that both rRNA and protein sequences analysed with advanced, realistic models of molecular evolution 6,7 provide independent support for two phases in the history of environmental temperature changes over the tree of life: in the first period, thermotolerance increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and of Archaea-Eukaryota; in the second period, it decreased. Therefore, the two lineages descending from LUCA and leading to the ancestors of Bacteria and Archaea-Eukaryota convergently adapted to high temperatures, maybe in response to a climate change of the early Earth 1,8,9 , and/or aided by the transition from an RNA genome in LUCA to organisms with more thermostable DNA genomes 10,11 . This analysis unifies apparently contradictory results 2-4 into a coherent depiction of the evolution of an ecological trait over the entire tree of life. Was LUCA a hyperthermophilic, i.e., with optimal growth temperature (OGT) ≥ 80 °C, thermophilic (80 °C ≥ OGT ≥ 50 °C), or mesophilic (OGT ≤ 50 °C) organism? Several investigations of this question have relied on correlations between the species OGT and the composition of their macromolecular sequences. In extant prokaryotic species, the G+C content of ribosomal RNA (rRNA) stems (i.e., double-stranded parts) has been shown to correlate with OGT 12 . Exploiting this correlation, Galtier et al. obtained support for a non-hyperthermophilic LUCA 2 . In contrast, studies based on correlations between the composition of LUCA's proteins and OGT concluded in favour of a hyperthermophilic LUCA 13,14 and of hyperthermophilic ancestors for both Archaea and Bacteria. The discrepancy between these results could come from some unexplained incongruence between rRNA and proteins, or, as we shall see, from differences between employed evolutionary models. All three investigations 2,13,14 based their conclusions on comparisons of reconstructed ancestral sequence compositions with extant ones. Accurate modelling of the evolution of compositions is therefore crucial for such approaches. On one side, two of these studies 13,14 relied on homogeneous models of evolution which make the simplifying hypothesis that substitutions occur with constant probabilities along time and across all lineages. Had genomes and proteins evolved according to a homogeneous model, they would all share the same base and amino acid compositions. Clearly, rRNA 12 and protein sequences 15 do not. On the other side, Galtier et al. 2 relied on a branch-heterogeneous model of RNA sequence evolution. Branch-heterogeneous models are computationally more challenging but more realistic as they allow replacement or substitution probabilities to vary between lineages, and thus explicitly account
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