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Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus.

Croll D, Sanders IR - BMC Evol. Biol. (2009)

Bottom Line: Our data show that AMF from one field have undergone recombination but that clonal lineages coexist.This finding has important consequences for understanding AMF evolution, co-evolution of AMF and plants and highlights the potential for commercially introduced AMF inoculum recombining with existing local populations.Finally, our results reconcile seemingly contradictory studies on whether AMF are clonal or form recombining populations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Ecology & Evolution, Biophore building, University of Lausanne, Lausanne, Switzerland.daniel.croll@unil.ch

ABSTRACT

Background: Arbuscular mycorrhizal fungi (AMF) are important symbionts of most plant species, promoting plant diversity and productivity. This symbiosis is thought to have contributed to the early colonisation of land by plants. Morphological stasis over 400 million years and the lack of an observed sexual stage in any member of the phylum Glomeromycota led to the controversial suggestion of AMF being ancients asexuals. Evidence for recombination in AMF is contradictory.

Results: We addressed the question of recombination in the AMF Glomus intraradices by sequencing 11 polymorphic nuclear loci in 40 morphologically identical isolates from one field. Phylogenetic relationships among genotypes showed a reticulate network pattern providing a rationale to test for recombination. Five statistical tests predicted multiple recombinant regions in the genome of a core set of isolates. In contrast, five clonal lineages had fixed a large number of differences.

Conclusion: Our data show that AMF from one field have undergone recombination but that clonal lineages coexist. This finding has important consequences for understanding AMF evolution, co-evolution of AMF and plants and highlights the potential for commercially introduced AMF inoculum recombining with existing local populations. Finally, our results reconcile seemingly contradictory studies on whether AMF are clonal or form recombining populations.

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Phylogenetic relationships among multi-locus genotypes of G. intraradices. The neighbour-network using uncorrected p distance showed reticulate phylogenetic branching among a core set of genotypes. Substitutions and indel mutations were given equal weight in the analysis. Bootstrap support for branches above 90% is indicated in % of 1000 replicates. Roman numerals represent the different genotypes from one field (I–XI and XIII–XVIIII) and DAOM181602 (XII).
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Figure 1: Phylogenetic relationships among multi-locus genotypes of G. intraradices. The neighbour-network using uncorrected p distance showed reticulate phylogenetic branching among a core set of genotypes. Substitutions and indel mutations were given equal weight in the analysis. Bootstrap support for branches above 90% is indicated in % of 1000 replicates. Roman numerals represent the different genotypes from one field (I–XI and XIII–XVIIII) and DAOM181602 (XII).

Mentions: We first estimated the phylogenetic relationships among the genotypes to identify potentially recombining genotypes and clonal lineages. Then, a series of statistical tests were performed on sequences from all genotypes to test whether there is significant evidence of recombination in the population. By applying a neighbour-network algorithm [22] reticulate paths connecting the core genotypes could be observed (I–X, DAOM181602, XIII, XIV; Fig. 1). A reticulate pattern suggests that recombination among genotypes may have contributed to the evolution of the genotypes, but multiple alternative mechanisms such as lack of phylogenetic resolution or homoplasy may also contribute to a reticulate pattern [23]. However, if recombination occurred within the population it is most likely among the core group of genotypes connected through a network (Fig. 1). The core genotypes weakly clustered into two subgroups, but multiple branches connect the two subgroups (I, IV–X and II, III, XIII, XIV, DAOM181602 respectively; Fig. 1). Five genotypes (XI, XV–XVIII) were distinguished by a comparatively large number of mutations from the set of core genotypes with very high bootstrap support (100%; Fig. 1). Three more genotypes were significantly differentiated from the core genotypes, but branch lengths were considerably shorter (IX, DAOM181602, XIV; Fig. 1). The reticulate pattern among the genotypes was conserved if all indel polymorphisms were excluded from the analysis (see additional file 4). This confirms that potential recurrent mutations, due to a higher indel mutation rate observed in repeat-rich regions, do not qualitatively alter the results of the analysis. The reticulate pattern among the core genotypes was still observed when the strongly differentiated genotypes (XI, XV–XVIII) were excluded, and this further supports the evidence of recombination (see additional file 4).


Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus.

Croll D, Sanders IR - BMC Evol. Biol. (2009)

Phylogenetic relationships among multi-locus genotypes of G. intraradices. The neighbour-network using uncorrected p distance showed reticulate phylogenetic branching among a core set of genotypes. Substitutions and indel mutations were given equal weight in the analysis. Bootstrap support for branches above 90% is indicated in % of 1000 replicates. Roman numerals represent the different genotypes from one field (I–XI and XIII–XVIIII) and DAOM181602 (XII).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2630297&req=5

Figure 1: Phylogenetic relationships among multi-locus genotypes of G. intraradices. The neighbour-network using uncorrected p distance showed reticulate phylogenetic branching among a core set of genotypes. Substitutions and indel mutations were given equal weight in the analysis. Bootstrap support for branches above 90% is indicated in % of 1000 replicates. Roman numerals represent the different genotypes from one field (I–XI and XIII–XVIIII) and DAOM181602 (XII).
Mentions: We first estimated the phylogenetic relationships among the genotypes to identify potentially recombining genotypes and clonal lineages. Then, a series of statistical tests were performed on sequences from all genotypes to test whether there is significant evidence of recombination in the population. By applying a neighbour-network algorithm [22] reticulate paths connecting the core genotypes could be observed (I–X, DAOM181602, XIII, XIV; Fig. 1). A reticulate pattern suggests that recombination among genotypes may have contributed to the evolution of the genotypes, but multiple alternative mechanisms such as lack of phylogenetic resolution or homoplasy may also contribute to a reticulate pattern [23]. However, if recombination occurred within the population it is most likely among the core group of genotypes connected through a network (Fig. 1). The core genotypes weakly clustered into two subgroups, but multiple branches connect the two subgroups (I, IV–X and II, III, XIII, XIV, DAOM181602 respectively; Fig. 1). Five genotypes (XI, XV–XVIII) were distinguished by a comparatively large number of mutations from the set of core genotypes with very high bootstrap support (100%; Fig. 1). Three more genotypes were significantly differentiated from the core genotypes, but branch lengths were considerably shorter (IX, DAOM181602, XIV; Fig. 1). The reticulate pattern among the genotypes was conserved if all indel polymorphisms were excluded from the analysis (see additional file 4). This confirms that potential recurrent mutations, due to a higher indel mutation rate observed in repeat-rich regions, do not qualitatively alter the results of the analysis. The reticulate pattern among the core genotypes was still observed when the strongly differentiated genotypes (XI, XV–XVIII) were excluded, and this further supports the evidence of recombination (see additional file 4).

Bottom Line: Our data show that AMF from one field have undergone recombination but that clonal lineages coexist.This finding has important consequences for understanding AMF evolution, co-evolution of AMF and plants and highlights the potential for commercially introduced AMF inoculum recombining with existing local populations.Finally, our results reconcile seemingly contradictory studies on whether AMF are clonal or form recombining populations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Ecology & Evolution, Biophore building, University of Lausanne, Lausanne, Switzerland.daniel.croll@unil.ch

ABSTRACT

Background: Arbuscular mycorrhizal fungi (AMF) are important symbionts of most plant species, promoting plant diversity and productivity. This symbiosis is thought to have contributed to the early colonisation of land by plants. Morphological stasis over 400 million years and the lack of an observed sexual stage in any member of the phylum Glomeromycota led to the controversial suggestion of AMF being ancients asexuals. Evidence for recombination in AMF is contradictory.

Results: We addressed the question of recombination in the AMF Glomus intraradices by sequencing 11 polymorphic nuclear loci in 40 morphologically identical isolates from one field. Phylogenetic relationships among genotypes showed a reticulate network pattern providing a rationale to test for recombination. Five statistical tests predicted multiple recombinant regions in the genome of a core set of isolates. In contrast, five clonal lineages had fixed a large number of differences.

Conclusion: Our data show that AMF from one field have undergone recombination but that clonal lineages coexist. This finding has important consequences for understanding AMF evolution, co-evolution of AMF and plants and highlights the potential for commercially introduced AMF inoculum recombining with existing local populations. Finally, our results reconcile seemingly contradictory studies on whether AMF are clonal or form recombining populations.

Show MeSH
Related in: MedlinePlus