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Coalescent-based analysis distinguishes between allo- and autopolyploid origin in shepherd’s purse (Capsella bursa-pastoris)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
Department of Biology, York University.
Laboratory of Evolutionary Genomics, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences.
Laboratory of Evolutionary Genomics, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences.
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2012 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 7, 1721-1733 p.Article in journal (Refereed) Published
Abstract [en]

Polyploidization plays an important role in plant speciation. The most recent estimates 36 report that up to 15% of angiosperm speciation events and 31% in ferns are accompanied 37 by changes in ploidy level. Polyploids can arise either through autopolyploidy, when the 38 sets of chromosomes originate from a single species, or through allopolyploidy, when 39 they originate from different species. In this study we used two different coalescent-based 40 methods to determine the date and mode of the polyploidization event that led to the 41 tetraploid cosmopolitan weed, Capsella bursa-pastoris. We sampled 78 C. bursa-pastoris 42 accessions, and 53 and 43 accessions from the only two other members of this genus, C. 43 grandiflora and C. rubella, respectively, and sequenced these accessions at 14 unlinked 44 nuclear loci with locus-specific primers in order to be able to distinguish the two 45 homeologues in the tetraploid. A large fraction of fixed differences between 46 homeologous genes in C. bursa-pastoris are segregating as polymorphisms in C. 47 grandiflora, consistent with an autopolyploid origin followed by disomic inheritance. To 48 test this, we first estimated the demographic parameters of an isolation-with-migration 49 model in a pairwise fashion between C. grandiflora and both genomes of C. bursa- 50 pastoris and used these parameters in coalescent simulations to test the mode of origin of 51 C. bursa-pastoris. Secondly we used Approximate Bayesian Computation to compare an 52 allopolyploid and an autopolyploid model. Both analyses led to the conclusion that C. 53 bursa-pastoris originated less than one million years ago by doubling of the C. 54 grandiflora genome.

Place, publisher, year, edition, pages
2012. Vol. 29, no 7, 1721-1733 p.
Keyword [en]
autopoplyploidy, coalescent, Brassicaceae, Approximate bayesian computation, IM model
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-136786DOI: 10.1093/molbev/mss024ISI: 000305409000004OAI: oai:DiVA.org:uu-136786DiVA: diva2:377485

Kate R. St.Onge, John Paul Foxe, and Li Junrui have contributed equally to this work

Available from: 2010-12-14 Created: 2010-12-14 Last updated: 2014-04-22
In thesis
1. Demography and Polyploidy in Capsella
Open this publication in new window or tab >>Demography and Polyploidy in Capsella
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Studies of demography and population structure give insight into important evolutionary processes such as speciation and diversification. In the present work I perform such studies in the genus Capsella, which has three species: C. grandiflora, an outcrossing diploid, C. rubella a selfing diploid, and C. bursa-pastoris a selfing tetraploid. These three species make a good model system for evolutionary studies because they encompass two major plant evolutionary processes: mating system shifts and polyploidization. To conduct my studies I have gathered a large number of samples across the distributions of each species and scored them both phenotypically and genotypically: more specifically we measured flowering time and collected DNA sequence data.

In the tetraploid C. bursa-pastoris we applied an association mapping approach which takes population structure into account to search for genetic variation associated with variation in flowering time. Flowering time is an important and highly adaptive trait which is frequently subject to natural selection. We found evidence of association between flowering time and several single nucleotide polymorphisms (SNPs) within the flowering locus C (FLC) and cryptochrome 1 (CRY1). In the case of FLC these SNPs code for nonconsensus splice site variation in one of the two copies of the gene. The SNPs could potentially have functional consequences and our results imply that non-functionalization of duplicate genes could be an important source of phenotypic variation.

Using a novel coalescent based approach, we investigated the polyploid origin of C. bursa-pastoris and find evidence supporting a recent autopolyploid origin of this species. In the two diploid species, I use sequence data to investigate population structure and demographic history and to assess the effects of selfing on C. rubella. Observed patterns of population structure and genetic diversity in C. rubella can be explained by a combination of both demographic history and mating system. Observed patterns in C. grandiflora suggest that the investigated populations do not deviate strongly from the SNM, which has rarely been found in modern demographic studies.

Finally, we investigate the effect of sampling strategy on demographic inference. Extensive sampling both within and across our populations allow us to empirically test the effect of sampling strategy on demographic inference. We complement the empirical analysis with simulations and conclude that the effect of sampling strategy is in many cases weak compared with that of demographic events. Nevertheless, these effects are real and have the potential to lead to false inference and therefore sampling strategy should be carefully considered in demographic studies.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2010. 39 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 795
Approximate Bayesian Computation, Mating system, Brassicaceae, flowering time, genetic diversity, Evolution
National Category
Biological Sciences
urn:nbn:se:uu:diva-136696 (URN)978-91-554-7979-4 (ISBN)
Public defence
2011-02-04, Zootissalen, Evolutionary biology centre, Villavägen 9, Uppsala, 10:00 (English)
Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 725Available from: 2011-01-14 Created: 2010-12-14 Last updated: 2011-03-21Bibliographically approved

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