Phylogeography of Yersinia ruckeri reveals effects of past evolutionary events on the current strain distribution and explains variations in the global transmission of enteric redmouth (ERM) disease.

Asmine Bastardo,Carmen Ravelo,Jesús L. Romalde

doi:10.3389/fmicb.2015.01198

Asmine Bastardo, Carmen Ravelo + Show 1 more

Open Access

https://doi.org/10.3389/fmicb.2015.01198

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Abstract

Phylogeographic patterns and population genetic structure of Yersinia ruckeri, the pathological agent of enteric redmouth disease (ERM) in salmonids, were investigated on the basis of concatenated multiloci sequences from isolates of different phenotypes obtained between 1965 and 2009 from diverse areas and hosts. Sequence analyses revealed genetic differentiation among subpopulations with the largest genetic distance occurring between subpopulations of Europe and Canada and/or South America. Bayesian analysis indicated the presence of three ancestral population clusters. Mismatch distribution displayed signatures characteristic of changes in size due to demographic and spatial expansions in the overall Y. ruckeri population, and also in the geographically separate subpopulations. Furthermore, a weak signal of isolation by distance was determined. A significant positive correlation between genetic and geographical distances was observed. These results revealed that the population of Y. ruckeri has undergone both ancient and recent population changes that were probably induced by biogeography forces in the past and, much more recently, by adaptive processes forced by aquaculture expansion. These findings have important implications for future studies on Y. ruckeri population dynamics, on the potential role of genetic structure to explain variations in ERM transmission, and on the effect of past evolutionary events on current estimations of gene flow.

Highlights

Studies on the evolutionary history of organisms have benefited from the availability of an increasing amount of data, especially multiple whole genome sequences
Each sequence type (ST) was considered as one haplotype, and the 103 isolates of Y. ruckeri were considered as one population, which were divided into nine different subpopulations on the basis of the geographical site of isolation as designated in the multilocus sequence typing (MLST) database (Table 1)
Biogeographical and inferred dispersal patterns of Y. ruckeri population were analyzed on a global scale using multi-sequence data

Summary

Introduction

Studies on the evolutionary history of organisms have benefited from the availability of an increasing amount of data, especially multiple whole genome sequences. This fact has led to more accurate reconstructions of phylogenetic relationships within several bacterial species (Pritchard et al, 2000). Sequence data provide direct genealogical information that can be efficiently used to estimate phylogenetic relationships and parameters associated with population dynamics. Despite the limitations of multilocus sequence typing (MLST) and eBURST analysis for the phylogenetic inferences to determine exact relationships between individual isolates (Castro-Nallar et al, 2015), large MLST data set represent a valuable resource from which population level trends can be obtained. Analysis of allele frequencies can facilitate recognition of distinct populations, and the comparisons of allelic diversity among populations are informative since ancient populations are expected to be more diverse than recent populations (Slatkin and Hudson, 1991; van Gremberghe et al, 2011)

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