Using principle component analysis to compare genetic diversity across polyploidy levels within plant complexes: an example from British Restharrows (Ononis spinosa and Ononis repens)

Kloda, Jane M.; Dean, P.D.G.; Maddren, C; MacDonald, D; Mayes, Sean

doi:10.1038/sj.hdy.6801044

Cited by 40 publications

(33 citation statements)

References 54 publications

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“…As a first approximation, we have treated these markers as dominant molecular traits, as has been done in other similar studies (for example, Kloda et al, 2008;Vanderpoorten et al, 2011;Sampson and Byrne, 2012). This resulted in simpler mixedploidy analyses and interpretation at the cost of a potential loss of information that could be obtained by exploiting the codominant nature of microsatellites and STS's.…”

Section: Utility Of Genetic Markers For Further Studymentioning

confidence: 99%

“…Raw peak sizes were analysed in a modified version of MsatAllele (Alberto, 2009) As the assumptions of traditional population genetic techniques cannot be easily met in mixed ploidy hybrid data sets, we used a presence-absence approach where the observed multilocus phenotypes are transformed to an allele matrix in which each allele is scored as either present or absent in each individual, similar to an amplified fragment length polymorphism (AFLP) profile. Further justification for use of this type of analysis for codominant markers in polyploid species can be found in Kloda et al (2008), Vanderpoorten et al (2011), and Sampson and Byrne (2012).…”

Section: Genetic Analysismentioning

confidence: 99%

“…To complement the DAPC results, we conducted a principal coordinate analysis of a matrix of pairwise genetic distances between individuals, as has been done for other studies of codominant data in polyploids (Kloda et al, 2008;Sampson and Byrne, 2012). This analysis does not require a priori assumptions of population membership, but simply represents the genetic (dis-)similarity among individuals.…”

Section: Population Genetic Structurementioning

confidence: 99%

“…We applied three complementary methods to analyse the patterns of population genetic structure in British Mimulus: (1) a discriminant analysis of principal components (DAPCs; Jombart et al, 2010); (2) a principal coordinate analyses of genetic similarity indices (Kloda et al, 2008); and (3) a hierarchical analysis of molecular variance (AMOVA; Excoffier et al, 1992). We describe each of these approaches below.…”

Section: Population Genetic Structurementioning

confidence: 99%

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Hybridisation and genetic diversity in introduced Mimulus (Phrymaceae)

Vallejo-Marin

Lye²

2012

Heredity

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Hybridisation among taxa with different ploidy levels is often associated with hybrid sterility. Clonal reproduction can stabilise these hybrids, but pervasive clonality may have a profound impact on the distribution of genetic diversity in natural populations. Here we investigate a widespread triploid taxon resulting from hybridisation between diploid Mimulus guttatus and tetraploid Mimulus luteus, two species that were introduced into the United Kingdom (UK) in the nineteenth century. This hybrid, Mimulus x robertsii, is largely sterile but capable of prolific vegetative propagation and has been recorded in the wild since 1872. We surveyed 40 Mimulus populations from localities across the UK to examine the current incidence of hybrids, and selected seventeen populations for genetic analysis using codominant markers. Cluster analyses revealed two main groups of genetically distinct individuals, corresponding to either diploid (M. guttatus) or polyploid (M. luteus and M. x robertsii) samples. Triploid hybrids were found in around 50% of sampled sites, sometimes coexisting with one of the parental species (M. guttatus). The other parent, M. luteus, was restricted to a single locality. Individual populations of M. x robertsii were genetically variable, containing multiple, highly heterozygous clones, with the majority of genetic variation distributed among-rather than within populations. Our findings demonstrate that this largely sterile, clonal taxon can preserve non-negligible amounts of genetic variation. The presence of genetically variable hybrid populations may provide the material for the continued success of asexual taxa in diverse environments.

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Section: Utility Of Genetic Markers For Further Studymentioning

confidence: 99%

Section: Genetic Analysismentioning

confidence: 99%

Section: Population Genetic Structurementioning

confidence: 99%

Section: Population Genetic Structurementioning

confidence: 99%

See 2 more Smart Citations

Hybridisation and genetic diversity in introduced Mimulus (Phrymaceae)

Vallejo-Marin

Lye²

2012

Heredity

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“…As a result, species or species complexes consisting of several independent cytotypes have been documented in many families (for example, Buggs and Pannell, 2007;Halverson et al, 2008;Kloda et al, 2008;Trávníček et al, 2010;Münzbergová et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Absence of gene flow between diploids and hexaploids of Aster amellus at multiple spatial scales

2012

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The potential for gene exchange across ploidy levels has long been recognized, but only a few studies have explored the rate of gene flow among different cytotypes. In addition, most of the existing knowledge comes from contact zones between diploids and tetraploids. The purpose of this paper was to investigate relationships between diploid and hexaploid individuals within the Aster amellus aggregate. A. amellus is known to occur in diploid and hexaploid cytotypes in Europe, with a complex contact zone in central Europe. Patterns of genetic diversity were investigated using seven microsatellite loci at three different spatial scales: (1) in the single known mixed-ploidy population; (2) in populations at the contact zone and (3) in a wider range of populations across Europe. The results show clear separation of the cytotypes at all three spatial scales. In addition, analysis of molecular variance strongly supported a model predicting a single origin of the hexaploids, with no or very limited gene flow between the cytotypes. Some hexaploid individuals found in the mixed-ploidy population, however, fell into the diploid cluster. This could suggest recurrent polyploid formation or occasional cross-pollination between cytotypes; however, there are strong post-zygotic breeding barriers between the two cytotypes, making the latter less plausible. Overall, the results suggest that the cytotypes could represent two cryptic species. Nevertheless, their formal separation is difficult as they cannot be distinguished morphologically, occupy very similar habitat conditions and have largely overlapping distribution ranges. These results show that polyploid complexes must be treated with caution as they can hide biological diversity and can have different adaptation potentials, evolving independently.

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Genetic differentiation and spatiotemporal history of diploidy and tetraploidy of Clintonia udensis

Wang

Fan

et al. 2017

Ecology and Evolution

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Polyploidy is an important factor shaping the geographic range of a species. Clintonia udensis (Clintonia) is a primary perennial herb widely distributed in China with two karyotypic characteristics—diploid and tetraploid and thereby used to understand the ploidy and distribution. This study unraveled the patterns of genetic variation and spatiotemporal history among the cytotypes of C. udensis using simple sequence repeat or microsatellites. The results showed that the diploids and tetraploids showed the medium level of genetic differentiation; tetraploid was slightly lower than diploid in genetic diversity; recurrent polyploidization seems to have opened new possibilities for the local genotype; the spatiotemporal history of C. udensis allows tracing the interplay of polyploidy evolution; isolated and different ecological surroundings could act as evolutionary capacitors, preserve distinct karyological, and genetic diversity. The approaches of integrating genetic differentiation and spatiotemporal history of diploidy and tetraploidy of Clintonia udens would possibly provide a powerful way to understand the ploidy and plant distribution and undertaken in similar studies in other plant species simultaneously contained the diploid and tetraploid.

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Using principle component analysis to compare genetic diversity across polyploidy levels within plant complexes: an example from British Restharrows (Ononis spinosa and Ononis repens)

Cited by 40 publications

References 54 publications

Hybridisation and genetic diversity in introduced Mimulus (Phrymaceae)

Hybridisation and genetic diversity in introduced Mimulus (Phrymaceae)

Absence of gene flow between diploids and hexaploids of Aster amellus at multiple spatial scales

Genetic differentiation and spatiotemporal history of diploidy and tetraploidy of Clintonia udensis

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