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- St Onge, Kate, 1982-, et al.
(författare)
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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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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 29:7, s. 1721-1733
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Tidskriftsartikel (refereegranskat)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.
(författare)
-
Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems
- 2011
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 20:16, s. 3306-3320
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Tidskriftsartikel (refereegranskat)abstract
- Mating system and population history can both have large impacts on genetic diversity and population structure. Here, we use multilocus sequence data to investigate how these factors impact two closely related Brassicaceae species: the selfing Capsella rubella and the outcrossing C. grandiflora. To do this we have sequenced 16 loci in approximately 70 individuals from 7 populations of each species. Patterns of population structure differ strongly between the two species. In C. grandiflora we observe an isolation-by-distance pattern and identify three clearly delineated genetic groups. In C. rubella, where we estimate the selfing rate to 0.90-0.94, the pattern is less clear with some sampling populations forming separate genetic clusters while others are highly mixed. The two species also have highly divergent histories. In close agreement with previous studies, our analysis gives very strong support for a recent bottleneck (18,600 ya) in C. rubella, which most likely represents speciation from C. grandiflora. In C. grandiflora there is moderate support for the standard neutral model in 2 of 3 genetic clusters, while the third cluster shows evidence of weak expansion. It is clear that mating system has an impact on these two species, for example affecting the level of genetic variation, genetic structure and potentially also the size of the bottleneck in C. rubella. However, our results also clearly show that a combination of past and present processes, some of which are not affected by mating system, are needed to explain the differences between C. rubella and C. grandiflora.
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| 3. |
- St.Onge, Kate, 1982-
(författare)
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Demography and Polyploidy in Capsella
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 4. |
- St.Onge, Kate, 1982-, et al.
(författare)
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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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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 2:7, s. 803-814
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Tidskriftsartikel (refereegranskat)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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