Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology

Huelsenbeck, John P.; Ronquist, Fredrik; Nielsen, Rasmus; Bollback, Jonathan P.

doi:10.1126/science.1065889

Cited by 2,372 publications

(1,380 citation statements)

References 31 publications

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“…Given that previously recognized NJ p ‐distance methods that identified PCV2 genotype were questioned by Franzo et al,15 we explored the phylogenetic history of PCV3 based on recent outbreak strains 41, 42. For the genotype identification of PCV3, three different algorithms, NJ, ML, and MCC, were used and two stable clades were identified (PCV3a and PCV3b).…”

Section: Discussionmentioning

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: Discussionmentioning

confidence: 99%

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

et al. 2018

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“…Then, for cyt-b, Bayesian analyses were conducted using MrBayes version 3.0 b4 (Huelsenbeck et al, 2001), which performs Metropolis-coupled Markov chain Monte Carlo analysis. A GTR model was used, with an among-site rate variation following a gamma distribution.…”

Section: Phylogenetic Methodsmentioning

confidence: 99%

Pliocene and Pleistocene diversification and multiple refugia in a Eurasian shrew (Crocidura suaveolens group)

Dubey

Zaitsev

Cosson

et al. 2006

Molecular Phylogenetics and Evolution

110

117

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We sequenced 998 base pairs (bp) of mitochondrial DNA cytochrome b and 799 bp of nuclear gene BRCA1 in the Lesser white-toothed shrew (Crocidura suaveolens group) over its geographic range from Portugal to Japan. The aims of the study were to identify the main clades within the group and respective refugia resulting from Pleistocene glaciations. Analyses revealed the Asian lesser white-toothed shrew (C. shantungensis) as the basal clade, followed by a major branch of C. suaveolens, subdivided sensu stricto into six clades, which split-up in the Upper Pliocene and Lower Pleistocene (1.9-0.9 Myr). The largest clade, occurring over a huge range from east Europe to Mongolia, shows evidence of population expansion after a bottleneck. West European clades originated from Iberian and Italo-Balkanic refugia. In the Near East, three clades evolved in an apparent hotspot of refugia (west Turkey, south-west and south-east of the Caucasus). Most clades include specimens of diVerent morphotypes and the validity of many taxa in the C. suaveolens group has to be re-evaluated. 

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“…Evolutionary Biology Centre, Uppsala University) was used to determine the best nucleotide substitution model. Phylogenetic analyses were then performed with MrBayes v. 3.1 (Huelsenbeck et al, 2001;Ronquist and Huelsenbeck, 2003) applying a general time-reversible (GTR) substitution model with gamma (G) and proportion of invariable site (I) parameters to accommodate variable rates across sites. The Markov Chain Monte Carlo (MCMC) analysis of four chains started from random tree topology and lasted 1,000,000 generations.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum–Neofusicoccum ribis species complex

Sakalidis

Hardy

Burgess

2011

Molecular Phylogenetics and Evolution

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Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology

Cited by 2,372 publications

References 31 publications

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

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

Pliocene and Pleistocene diversification and multiple refugia in a Eurasian shrew (Crocidura suaveolens group)

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum–Neofusicoccum ribis species complex

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