A mathematical method for determining genome divergence and species delineation using AFLP.

Abstract

The delineation of bacterial species is presently achieved using direct DNA-DNA relatedness studies of whole genomes. It would be helpful to obtain the same genomically based delineation by indirect methods, provided that descriptions of individual genome composition of bacterial genomes are obtained and included in species descriptions. The amplified fragment length polymorphism (AFLP) technique could provide the necessary data if the nucleotides involved in restriction and amplification are fundamental to the description of genomic divergences. Firstly, in order to verify that AFLP analysis permits a realistic exploration of bacterial genome composition, the strong correspondence between predicted and experimental AFLP data was demonstrated using Agrobacterium strain C58 as a model system. Secondly, a method is proposed for determining current genome mispairing and evolutionary genome divergences between pairs of bacteria, based on arbitrary sampling of genomes by using AFLP. The measure of current genome mispairing was validated by comparison with DNA-DNA relatedness data, which itself correlates with base mispairing. The evolutionary genome divergence is the estimated rate of nucleotide substitution that has occurred since the strains diverged from a common ancestor. Current genome mispairing and evolutionary genome divergence were used to compare members of Agrobacterium, used as a model of closely related genomic species. A strong and highly significant correlation was found between calculated genome mispairing and DNA-DNA relatedness values within genomic species. The canonical 70 % DNA-DNA hybridization value used to delineate genomic species was found to correspond to a range of current genome mispairing of 13-136 %. These limits correspond to 0097 and 0104 nucleotide substitutions per site, respectively. In addition, experimental data showed that the large Ti and cryptic plasmids of Agrobacterium had little effect on the estimation of genome divergence. Evolutionary genome divergence was used for phylogenetic inferences. Data showed that members of the same genomic species clustered consistently, as supported by bootstrap resampling. On the basis of these results, it is proposed that the genomic delineation of bacterial species could be based, in future, on phylogenetic groups supported by bootstraps and genome descriptions of individual strains, obtained by AFLP analysis, recorded in accessible databases ; this approach might eventually replace DNA-DNA hybridization studies.

AFLPs support deep relationships among darters (Percidae: Etheostomatinae) consistent with morphological hypotheses

“…Genetic distances estimated by two restriction-site distance metrics, DiceJC and PAUP* Nei-Li, are strongly correlated (r ¼ 1.00); however, PAUP* Nei-Li distances yield a greater amount of scatter around the regression line of distance on shared bands as compared with DiceJC distances (Supplementary Figure 1). This scatter suggests that PAUP* generated Nei-Li distances may not as accurately reflect genetic relationships, and perhaps suggests that, as shown by Mougel et al (2002), constraining nucleotides are important in calculations of genomic divergence. Importantly, however, neither the topology (with the exception of one species, E. radiosum) nor the statistical support of nodes in the neighborjoining tree based on PAUP* Nei-Li distances were noticeably different from the DiceJC tree.…”

“…Restriction-site distance methods can be used with AFLP fragments because AFLP bands show a similar statistical behavior to restriction site data (Mougel et al, 2002). Genetic distances estimated by two restriction-site distance metrics, DiceJC and PAUP* Nei-Li, are strongly correlated (r ¼ 1.00); however, PAUP* Nei-Li distances yield a greater amount of scatter around the regression line of distance on shared bands as compared with DiceJC distances (Supplementary Figure 1).…”

“…In addition, we propose an AFLP molecular clock based on previous studies that used sequence data calibrated to the absolute age of fossils of centrarchid fishes (Near and Benard, 2004;Near and Keck, 2005;Hollingsworth and Near, 2009). Finally, we show that the AFLP distance measures described by Mougel et al (2002) may provide a more precise estimate of genetic distance than the more traditionally used Nei-Li equation.…”

“…The matrix was translated into a distance matrix using the Dice distance equation with a Jukes-Cantor correction and 18 constraining nucleotides as described by Mougel et al (2002) using DistAFLP (available from http://pbil.univ-lyon1.fr/ADE-4/microb). The Dice distance equation with constraining nucleotides is as follows: …”

Rapid and Efficient Methods to Isolate, Type Strains and Determine Species of Agrobacterium spp. in Pure Culture and Complex Environments

“…biovar 3), A. rubi and A. larrymoorei have been validated as bona fide species (Ophel & Kerr, 1990;Holmes & Roberts, 1981;Bouzar & Jones, 2001). For its part biovar 1 is heterogeneous, including ten genomospecies (De Ley, 1973, 1974Popoff et al, 1984) currently called genomovar G1 to G9 (Mougel et al, 2002) and G13 (Portier et al, 2006 ). Biovar 1 is thus a species complex and not a single bacterial species.…”