surviving the game of dating - Relaxed phylogenetics and dating with confidence 2016

A global molecular clock cannot be assumed for any gene. doi: 10.1093/molbev/mst064 Pub Med Abstract | Cross Ref Full Text | Google Scholar Zuckerkandl, E., and Pauling, L. “Evolutionary divergence and convergence in proteins,” in Evolving Genes and Proteins, eds V. The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice.From the chronograms obtained, we carried out a diversification analysis using several approaches. No use, distribution or reproduction is permitted which does not comply with these terms.Following the publications of Zuckerkandl and Pauling (1965) and Kimura (1968), molecular dating has been based on the molecular clock hypothesis of a constant chronological rate of sequence change (Lemey and Posada, 2009).

Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available.

More recently, several methods based on molecular sequence data have been developed to estimate speciation and extinction rates from phylogenies reconstructed from contemporary taxa.

The results suggest that the genus Aeromonas began to diverge approximately 250 millions of years (Ma) ago.

All methods used to determine Aeromonas diversification gave similar results, suggesting that the speciation process in this bacterial genus followed a rate-constant (Yule) diversification model, although there is a small probability that a slight deceleration occurred in recent times. doi: 10.1016/j.ympev.20 Pub Med Abstract | Cross Ref Full Text | Google Scholar Xia, X. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.

There are only a few references in the literature about bacterial diversification (Martin et al., 2004; Vinuesa et al., 2005; Barraclough et al., 2009; Morlon et al., 2012; Lorén et al., 2014), and in no case has the reported analysis been as complete as those published on higher organisms.

Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa.

We also determined the constant of diversification (λ) values, which in all cases were very similar, about 0.01 species/Ma, a value clearly lower than those described for different eukaryotes.

Prokaryotes are an essential and largely unnoticed component of the earth’s biota.

The genus Aeromonas Stanier 1943 (Martin-Carnahan and Joseph, 2005) is a Gammaproteobacteria (Proteobacteria, Bacteria) that comprises a group of Gram-negative, rod-shaped bacteria, which are autochthonous to aquatic environments worldwide and are usual microbiota (as well as primary or secondary pathogens) of fish, amphibians and other animals (Janda and Abbott, 2010). We used the divergence time of Escherichia coli and Salmonella enterica as the calibration point.

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