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1.
  • Säll, T., et al. (creator_code:aut_t)
  • Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica
  • 2003
  • record:In_t: Journal of Evolutionary Biology. - : John Wiley & Sons Inc.. - 1010-061X .- 1420-9101. ; 16:5, s. 1019-1029
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • DNA sequencing was performed on up to 12 chloroplast DNA regions [giving a total of 4288 base pairs (bp) in length] from the allopolyploid Arabidopsis suecica (48 accessions) and its two parental species, A. thaliana (25 accessions) and A. arenosa (seven accessions). Arabidopsis suecica was identical to A. thaliana at all 93 sites where A. thaliana and A. arenosa differed, thus showing that A. thaliana is the maternal parent of A. suecica. Under the assumption that A. thaliana and A. arenosa separated 5 million years ago, we estimated a substitution rate of 2.9 x 10(-9) per site per year in noncoding single copy sequence. Within A. thaliana we found 12 substitution (single bp) and eight insertion/deletion (indel) polymorphisms, separating the 25 accessions into 15 haplotypes. Eight of the A. thaliana accessions from central Sweden formed one cluster, which was separated from a cluster consisting of central European and extreme southern Swedish accessions. This latter cluster also included the A. suecica accessions, which were all identical except for one 5 bp indel. We interpret this low level of variation as a strong indication that A. suecica effectively has a single origin, which we dated at 20 000 years ago or more.
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2.
  • Jakobsson, Mattias, et al. (creator_code:aut_t)
  • A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers
  • 2006
  • record:In_t: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 23:6, s. 1217-1231
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • A coalescent-based method was used to investigate the origins of the allotetraploid Arabidopsis suecica, using 52 nuclear microsatellite loci typed in eight individuals of A. suecica and 14 individuals of its maternal parent Arabidopsis thaliana, and four short fragments of genomic DNA sequenced in a sample of four individuals of A. suecica and in both its parental species A. thaliana and Arabidopsis arenosa. All loci were variable in A. thaliana but only 24 of the 52 microsatellite loci and none of the four sequence fragments were variable in A. suecica. We explore a number of possible evolutionary scenarios for A. suecica and conclude that it is likely that A. suecica has a recent, unique origin between 12,000 and 300,000 years ago. The time estimates depend strongly on what is assumed about population growth and rates of mutation. When combined with what is known about the history of glaciations, our results suggest that A. suecica originated south of its present distribution in Sweden and Finland and then migrated north, perhaps in the wake of the retreating ice.
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3.
  • Jakobsson, Mattias, et al. (creator_code:aut_t)
  • Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana
  • 2007
  • record:In_t: Theoretical and Applied Genetics. - : Springer. - 0040-5752 .- 1432-2242. - 0040-5752 ; 114:2, s. 223-235
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated-such as the position of a locus within the chromosome, or imperfect repeats-appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.
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4.
  • Jakobsson, Mattias, et al. (creator_code:aut_t)
  • Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana
  • 2007
  • record:In_t: Theoretical And Applied Genetics. - : Springer Science and Business Media LLC. - 0040-5752 .- 1432-2242. ; 114:2, s. 223-235
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated-such as the position of a locus within the chromosome, or imperfect repeats-appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.
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5.
  • Jakobsson, Mattias, et al. (creator_code:aut_t)
  • The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica.
  • 2007
  • record:In_t: Journal of evolutionary biology. - : Wiley. - 1420-9101 .- 1010-061X. ; 20:1, s. 104-121
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The evolutionary history of the common chloroplast (cp) genome of the allotetraploid Arabidopsis suecica and its maternal parent A. thaliana was investigated by sequencing 50 fragments of cpDNA, resulting in 98 polymorphic sites. The variation in the A. suecica sample was small, in contrast to that of the A. thaliana sample. The time to the most recent common ancestor (T-MRCA) of the A. suecica cp genome alone was estimated to be about one 37th of the T-MRCA of both the A. thaliana and A. suecica cp genomes. This corresponds to A. suecica having a MRCA between 10 000 and 50 000 years ago, suggesting that the entire species originated during, or before, this period of time, although the estimates are sensitive to assumptions made about population size and mutation rate. The data was also consistent with the hypothesis of A. suecica being of single origin. Isolation-by-distance and population structure in A. thaliana depended upon the geographical scale analysed; isolation-by-distance was found to be weak on the global scale but locally pronounced. Within the genealogical cp tree of A. thaliana, there were indications that the root of the A. suecica species is located among accessions of A. thaliana that come primarily from central Europe. Selective neutrality of the cp genome could not be rejected, despite the fact that it contains several completely linked protein-coding genes.
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6.
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7.
  • Säll, Torbjörn, et al. (creator_code:aut_t)
  • Mode of reproduction in Arabidopsis suecica
  • 2004
  • record:In_t: Hereditas. - : Springer Science and Business Media LLC. - 1601-5223 .- 0018-0661. ; 141:3, s. 313-317
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The breeding system of Arabidopsis suecica was investigated through genetic analysis of microsatellite segregation patterns in Five controlled crosses as well as in 16 single-mother families collected in the wild. Analysis of single and two-locus segregations in the F-2 generation following a cross clearly shows that A. suecica is reproduces sexually. The single-mother families show a high level of homozygosity corroborating earlier results indicating a high level of inbreeding. The high level of individual homozygosity is due both to a high level of selfing and to the underlying population structure.
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