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Taming the wild: resolving the gene pools of non-model Arabidopsis lineages.

Hohmann N, Schmickl R, Chiang TY, Lučanová M, Kolář F, Marhold K, Koch MA - BMC Evol. Biol. (2014)

Bottom Line: The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry.The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins.Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.

View Article: PubMed Central - PubMed

Affiliation: Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany. nora.hohmann@cos.uni-heidelberg.de.

ABSTRACT

Background: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses.

Results: Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins.

Conclusions: Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.

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Growth form of variousArabidopsisspecies. Growth form of selected Arabidopsis species. A)Arabidopsis pedemontana, B)Arabidopsis halleri, C)Arabidopsis cebennensis (photographs taken by MA Koch (©), U Wagenfeld; Heidelberg).
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Fig6: Growth form of variousArabidopsisspecies. Growth form of selected Arabidopsis species. A)Arabidopsis pedemontana, B)Arabidopsis halleri, C)Arabidopsis cebennensis (photographs taken by MA Koch (©), U Wagenfeld; Heidelberg).

Mentions: A. cebennensis, A. pedemontana and A. croatica have distinct highly endemic European distribution ranges (NE Italy, SW France and the Velebit mountains in Croatia, respectively). The species also differ markedly in their ecological preferences and morphology, all of which correlates with the deeper phylogenetic splits inferred among these taxa (Figure 2) and the biogeographic affinity of A. pedemontana and A. cebennensis to A. halleri and of A. croatica to A. arenosa and A. lyrata. Arabidopsis pedemontana and A. cebennensis share some traits with A. halleri, such as extensive clonal growth, preference for higher moisture, longevity and occurrence at high. Additionally, there is also a striking correlation with phenology, with increasing plant height from A. halleri, A. pedemontana towards A. cebennensis (up to 1.50 m tall), and increased preference of continuously available and cool streaming water in the same sequence of species (Figure 6).Figure 6


Taming the wild: resolving the gene pools of non-model Arabidopsis lineages.

Hohmann N, Schmickl R, Chiang TY, Lučanová M, Kolář F, Marhold K, Koch MA - BMC Evol. Biol. (2014)

Growth form of variousArabidopsisspecies. Growth form of selected Arabidopsis species. A)Arabidopsis pedemontana, B)Arabidopsis halleri, C)Arabidopsis cebennensis (photographs taken by MA Koch (©), U Wagenfeld; Heidelberg).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4216345&req=5

Fig6: Growth form of variousArabidopsisspecies. Growth form of selected Arabidopsis species. A)Arabidopsis pedemontana, B)Arabidopsis halleri, C)Arabidopsis cebennensis (photographs taken by MA Koch (©), U Wagenfeld; Heidelberg).
Mentions: A. cebennensis, A. pedemontana and A. croatica have distinct highly endemic European distribution ranges (NE Italy, SW France and the Velebit mountains in Croatia, respectively). The species also differ markedly in their ecological preferences and morphology, all of which correlates with the deeper phylogenetic splits inferred among these taxa (Figure 2) and the biogeographic affinity of A. pedemontana and A. cebennensis to A. halleri and of A. croatica to A. arenosa and A. lyrata. Arabidopsis pedemontana and A. cebennensis share some traits with A. halleri, such as extensive clonal growth, preference for higher moisture, longevity and occurrence at high. Additionally, there is also a striking correlation with phenology, with increasing plant height from A. halleri, A. pedemontana towards A. cebennensis (up to 1.50 m tall), and increased preference of continuously available and cool streaming water in the same sequence of species (Figure 6).Figure 6

Bottom Line: The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry.The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins.Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.

View Article: PubMed Central - PubMed

Affiliation: Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany. nora.hohmann@cos.uni-heidelberg.de.

ABSTRACT

Background: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses.

Results: Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins.

Conclusions: Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.

Show MeSH
Related in: MedlinePlus