FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

Murrell, Ben; Moola, Sasha; Mabona, Amandla; Weighill, Thomas; Sheward, Daniel J.; Pond, Sergei L. Kosakovsky; Scheffler, Konrad

doi:10.1093/molbev/mst030

Cited by 1,118 publications

(1,024 citation statements)

References 40 publications

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“…The methods used to investigate positive codon sites included FEL, SLAC, FUBAR, MEME,62, 63, 64 the branch site REL and the GA‐branch site models were chosen to determine the selection pressure on the individual branches 65, 66. Methods with p < 0.1 in SLAC, p < 0.05 in FEL and MEME and the posterior probability >0.9 in FUBAR, were considered to be more conservative positive selection pressure.…”

Section: Methodsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

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Porcine circovirus 3 (PCV3) is a novel virus associated with acute PDNS (porcine dermatitis and nephropathy syndrome)‐like clinical signs identified by metagenomic sequencing from swine. Its high occurrence may pose a potential threat to the swine industry worldwide. The processes resulting in the emergence and spread of PCV3 remain poorly understood. Herein, the possible origin, genotypes, and evolutionary dynamics of PCV3 based on available genomic sequences are determined. The closest ancestor of PCV3 is found to be within the clade 1 bat CVs. Using different phylogenetic methods, two major genotypes are identified, PCV3a and PCV3b. It is found that the effective population size of PCV3 increased rapidly during late 2013 to early 2014 and this is associated with the diversification of PCV3a and PCV3b. A relatively high effective reproductive number (Re) value and higher evolutionary rate were found compared to other single‐stranded DNA viruses, and positive selection on codons 122 and 320 (24 of ORF2) is identified. It is hypothesized that this, together with the prediction of a potential change of an antigenic epitope at position 320, might have allowed PCV3 to escape from the host immune response. Overall, this study has important implications for understanding the ongoing PCV3 cases worldwide and will guide future efforts to develop effective preventive and control measures.

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Section: Methodsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

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“…We further implemented likelihood and Bayesian-based methods to identify site-specific Cytb positive selection where the rate of non-synonymous substitution (dN) is greater than the rate of synonymous substitution (dS). We applied a suit of different algorithms for selection inference to our data: single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL) [30], internal fixed effects likelihood (IFEL) [31], fast unconstrained Bayesian approximation (FUBAR) [32] and mixed effects model of evolution (MEME) [33] to our data. SLAC is based on the reconstruction of the ancestral sequences and the counts of dS and dN at each codon position of the phylogeny.…”

Section: Methodsmentioning

confidence: 99%

Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

et al. 2014

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Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy.

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“…In addition to CODEML models, we used the programme HyPhy implemented in the web-server Datamonkey (Delport et al, 2010) to identify codons putatively under selection using Fast Unconstrained Bayesian AppRoximation (FUBAR; Murrell et al, 2013) and Mixed Effects Model of Evolution (MEME; Murrell et al, 2012). FUBAR assigns each codon a posterior probability (PP) of belonging to three classes of ω: ω 0 o1, ω 1 = 1 and ω 0 41.…”

Section: Divergence Time Estimatesmentioning

confidence: 99%

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

et al. 2016

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Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in geneticsbased metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid-to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.

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FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

Cited by 1,118 publications

References 40 publications

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

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