| 1. |
- St Onge, Kate, 1982-, et al.
(author)
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Coalescent-based analysis distinguishes between allo- and autopolyploid origin in shepherd’s purse (Capsella bursa-pastoris)
- 2012
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In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 29:7, s. 1721-1733
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Journal article (peer-reviewed)abstract
- 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.
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| 2. |
- St.Onge, Kate, 1982-, et al.
(author)
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The impact of sampling schemes on demographic inference : an empirical study in two species with different mating systems and demographic histories
- 2012
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 2:7, s. 803-814
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Journal article (peer-reviewed)abstract
- Most species have at least some level of genetic structure. Recent simulation studies have shown that it is important to consider population structure when sampling individuals to infer past population history. This is because different sampling strategies will introduce biases in the site frequency spectrum (SFS), which is generally the basic information used to infer population history. The relevance of the results of these computer simulations for empirical studies, however, remains unclear. In the present study we use DNA sequence datasets collected in two closely related species with very different histories, the selfing species Capsella rubella and its outcrossing relative C. grandiflora, to assess the impact of different sampling strategies on summary statistics and the inference of historical demography. Sampling strategy did affect values of Tajima’s D in both species but differences were not significant, and the general conclusions about demographic history were comparable across sampling schemes even when re-sampled data were analysed with Approximate Bayesian Computation. We explore the effects of sampling scheme when a limited number of loci are analysed, and in models that include population expansion within demes and hierarchical structure. While we observe a less severe effect of sampling than predicted under some simulation models, our results should not be seen as an encouragement to neglect this issue. In general, a good coverage of the natural range, both within and between populations, will be needed to obtain a reliable reconstruction of a species demographic history.
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