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  • 1.
    Alström-Rapaport, Cecilia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Leskinen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Parnilo, Pekka
    Seasonal variation in the mode of reproduction of Ulva intestinalis in a brackish water environment2010In: Aquatic Botany, ISSN 0304-3770, E-ISSN 1879-1522, Vol. 93, no 4, p. 244-249Article in journal (Refereed)
    Abstract [en]

    We explored the reproductive modes of Viva intestinalis in the inner part of the Baltic Sea during three consecutive years by using five microsatellite loci to estimate the relative abundance of diploid sporophytes and haploid gametophytes. Our results suggest that both diploid sporophytes and haploid gametophytes occur regularly in the Baltic Sea. The ratio of haploid to diploid individuals changes with seasons. Sporophytes are more abundant than gametophytes throughout the year, but the proportion of haploids increases from 10% in early summer to 35% in September. The over-wintering takes primarily place as diploid spores released by sporophytes. The sporophytes appear to reproduce both sexually and asexually in the Baltic Sea, since clones were found for this life phase. The fraction of individuals which belonged to an apparent diploid clone was higher in spring (62%) than in autumn (33%). We also found evidence for asexual clones in haploid gametophytes. The presence of both diploid and haploid individuals and the pattern of genetic and genotypic diversity provide evidence of sexual reproduction in the Baltic Sea. Thus the sporophytes and gametophytes do not function as two reproductively separate units. Compared with many other algal species with a reduced reproductive cycle in low salinity, U. intestinalis differs by having a multitude of reproductive modes also in the brackish water Baltic Sea, which can in part explain the dynamic propagation and high adaptability of the species.

  • 2. Berlin, Sofia
    et al.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    von Arnold, Sara
    Öst, Torbjörn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Rönnberg-Wästljung, Ann Christin
    High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus2010In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, no 1, p. 129-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Salix (willow) and Populus (poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the Populus trichocarpa genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya. RESULTS: We constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S1, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S3 consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41). CONCLUSIONS: The relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 x 10-9 and 1.68 x 10-9 per site and year, which are close to rates found in other perennials but much lower than rates in annuals.

  • 3.
    Cassel-Lundhagen, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Sjögren-Gulve, Per
    Limited dispersal by the rare scarce heath butterfly - potential consequences for population persistence2007In: Journal of Insect Conservation, ISSN 1366-638X, E-ISSN 1572-9753, Vol. 11, no 2, p. 113-121Article in journal (Refereed)
    Abstract [en]

    Dispersal between habitat patches may be important for the long-term persistence of populations. We conducted a mark-release-recapture study and analysed the dispersal pattern in the scarce heath butterfly inhabiting a network of suitable habitat patches using stepwise logistic regression (SLR) and the Virtual Migration (VM) model. We also analysed the influence of different types of matrices. We found that the majority of the recaptured butterflies remained within the patch where they were originally caught. However, dispersal between patches did occur and both the SLR analysis and the VM model indicated that the migration pattern was significantly associated with patch area and its level of isolation. The SLR model also showed that there was a positive association between immigration rate and tree density, supporting earlier observations that this species prefers semi-open habitat. We discuss the use of SLR versus the VM model to analyse recapture data in dispersal studies. This system is not at equilibrium, as a number of the most important patches in the network are continuously being lost due to afforestation and a number of populations are facing deterministic extinction. This increases the risk of a chain reaction of local extinctions, which may cause a collapse of the whole system.

  • 4.
    Hagenblad, Jenny
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Olsson, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Parker, Heidi G.
    Ostrander, Elaine A.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Population genomics of the inbred Scandinavian wolf2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, no 7, p. 1341-1351Article in journal (Refereed)
    Abstract [en]

    The Scandinavian wolf population represents one of the genetically most well-characterized examples of a severely bottlenecked natural population (with only two founders), and of how the addition of new genetic material (one immigrant) can at least temporarily provide a 'genetic rescue'. However, inbreeding depression has been observed in this population and in the absence of additional immigrants, its long-term viability is questioned. To study the effects of inbreeding and selection on genomic diversity, we performed a genomic scan with approximately 250 microsatellite markers distributed across all autosomes and the X chromosome. We found linkage disequilibrium (LD) that extended up to distances of 50 Mb, exceeding that of most outbreeding species studied thus far. LD was particularly pronounced on the X chromosome. Overall levels of observed genomic heterozygosity did not deviate significantly from simulations based on known population history, giving no support for a general selection for heterozygotes. However, we found evidence supporting balancing selection at a number of loci and also evidence suggesting directional selection at other loci. For markers on chromosome 23, the signal of selection was particularly strong, indicating that purifying selection against deleterious alleles may have occurred even in this very small population. These data suggest that population genomics allows the exploration of the effects of neutral and non-neutral evolution on a finer scale than what has previously been possible.

  • 5.
    Hemmilä, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Kumara, M.
    Ravikanth, G.
    Gustafsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Vasudeva, R.
    Ganeshaiah, K. N.
    Uma Shaanker, R.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Development of eleven microsatellite markers in the red-listed tree species Myristica malabarica2010In: Conservation Genetics Resources, ISSN 1877-7252, Vol. 2, no Suppl. 1, p. 305-307Article in journal (Refereed)
    Abstract [en]

    The Myristicaceae family is a primitive angiosperm family and is characterized by species that are highly endemic to the Western Ghats area of India. Myristica malabarica is confined to the evergreen forests of Western Ghats and Sri Lanka. In this paper we describe for the first time the development of eleven polymorhpic microsatellite markers for Myristica malabarica, which had 2–14 alleles per locus. These microsatellite markers could be used to study the population genetic structure of the species.

  • 6.
    Hemmilä, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Mohana Kumara, P.
    Ravikanth, G.
    Gustafsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Sreejayan, N.
    Vasudeva, R.
    Ganeshaiah, K. N.
    Uma Shaanker, R.
    Lascoux, Martin
    Development of polymorphic microsatellite loci in the endangered tree species Dysoxylum malabaricum2010Manuscript (preprint) (Other academic)
    Abstract [en]

    Dysoxylum malabaricum Bedd. (Meliaceae) is an economically important tree species occurring in the Western Ghats, a mega-diversity hotspot in southern India. In this paper, we report the development of fifteen microsatellite markers for D. malabaricum. The microsatellite primers development of fifteen microsatellite markers for D. malabaricum. The microsatellite primers screened had 2-9 alleles per locus and the observed and expected heterozygosity ranged from 0.07 to 1.00 and 0.07 to 0.9 respectively. Seven microsatellites cross amplified in the related species Dysoxylum binectariferum and showed good polymorphism. These are the first microsatellites described for D. malabaricum and they will be used to study population structure and genetic diversity.

  • 7. Lönn, Mikael
    et al.
    Alexandersson, Ronny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Gustafsson, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Hybrids and fruit set in a mixed flowering-time population of Gymnadenia conopsea (Orchidaceae)2006In: Hereditas, ISSN 0018-0661, E-ISSN 1601-5223, Vol. 143, no 1, p. 222-228Article in journal (Refereed)
    Abstract [en]

    We have recently found that the morphologically determined subspecies Gymnadenia conopsea ssp conopsea in Sweden includes early and late flowering individuals. We were interested in the interactions between the flowering time groups; if there were gene flow between them and if so this was detrimental or advantageous. A spatially mixed population of early and late flowering individuals was studied using three microsatellite loci. We measured patterns in genetic differentiation and inferred occurrence of hybridisation and introgression. Variation in flowering time, fertility and relative and absolute fruit set was measured. The pattern of introgression between flowering-time groups differed between loci. In two of the three investigated loci, allele separation was distinct between early and late flowering plants and one genetically obvious hybrid was infertile. In the third locus, several alleles were shared between the two flowering time variants. The degree of introgression was associated to fruit set failure, which was higher in the late flowering plants and lower in early flowering plants. A small group of early flowering individuals with somewhat delayed flowering compared to the main group was genetically distinct and had lower relative and absolute fruit set. This group was not genetically intermediate, but rather constituting an independent group, with lower fruit set possibly caused by absence of pollinators. There seem to be a strong barrier against introgression into the late flowering group which is kept genetically distinct and less diverse. The early flowering group is diverse, includes two subgroups and seems to benefit from gene flow.

  • 8.
    Parducci, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Bennett, K.D.
    Ancient DNA studies in plant populations2010In: Molecular markers, PCR, bioinformatics and ancient DNA-technology, troubleshooting and applications / [ed] Dorado, G., Cordoba: Cordoba University , 2010Chapter in book (Refereed)
  • 9.
    Parducci, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Suyama, Y.
    Single-pollen genotyping of Holocene lake sediments2010In: Single-pollen genotyping / [ed] Isagi, Y. & Suyama, Y., Springer-Verlag Tokyo Inc., 2010Chapter in book (Refereed)
  • 10. Ruokonen, M.
    et al.
    Aarvak, T.
    Chesser, R. K.
    Lundqvist, Anna-Carin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Merila, J.
    Temporal increase in mtDNA diversity in a declining population2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 12, p. 2408-2417Article in journal (Refereed)
    Abstract [en]

    In small and declining populations levels of genetic variability are expected to be reduced due to effects of inbreeding and random genetic drift. As a result, both individual fitness and populations' adaptability can be compromised, and the probability of extinction increased. Therefore, maintenance of genetic variability is a crucial goal in conservation biology. Here we show that although the level of genetic variability in mtDNA of the endangered Fennoscandian lesser white-fronted goose Anser erythropus population is currently lower than in the neigbouring populations, it has increased sixfold during the past 140 years despite the precipitously declining population. The explanation for increased genetic diversity in Fennoscandia appears to be recent spontaneous increase in male immigration rate equalling 0.56 per generation. This inference is supported by data on nuclear microsatellite markers, the latter of which show that the current and the historical Fennoscandian populations are significantly differentiated (F-ST = 0.046, P = 0) due to changes in allele frequencies. The effect of male-mediated gene flow is potentially dichotomous. On the one hand it may rescue the Fennoscandian lesser white-fronted goose from loss of genetic variability, but on the other hand, it eradicates the original genetic characteristics of this population.

  • 11. Semerikova, Svetlana A.
    et al.
    Semerikov, Vladimir L.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Post-glacial history and introgression in Abies (Pinaceae) species of the Russian Far East inferred from both nuclear and cytoplasmic markers2011In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 38, no 2, p. 326-340Article in journal (Refereed)
    Abstract [en]

    Aim The main aim of the present study is to infer the post-glacial history of Abies species from north-east Asia and to test the hypotheses that coastal Abies populations suffered less from climatic fluctuations during Pleistocene glacial periods than their more continental counterparts, and that Sakhalin was a major area of introgression. Location Natural ranges of the fir species Abies nephrolepis, Abies sachalinensis and Abies holophylla in the Russian Far East, and of Abies gracilis, which is endemic to the Kamchatka Peninsula. Methods Nineteen populations were sampled for allozyme analysis. Seventeen of these populations were also screened for variation at two paternally inherited chloroplast DNA microsatellite loci (cpSSR) and variation at one maternally inherited mitochondrial marker (nad4-3/4). Finally a subset of 11 populations was analysed with amplified fragment length polymorphism (AFLP). Comparisons were made with already available Abies sibirica data. For all sets of markers, we estimated genetic diversity and differentiation using an analysis of molecular variance (AMOVA). Population clustering was assessed with a Bayesian approach implemented in structure v.2.3. Results Among the three major species, A. sibirica, A. nephrolepis and A. sachalinensis, A. sachalinensis demonstrated the highest cytoplasmic and nuclear diversity and the most continental species, A. sibirica, the lowest. Both nuclear and mitochondrial DNA markers revealed the presence of a transitional zone on Sakhalin Island between A. nephrolepis and A. sachalinensis of south Sakhalin. The structure analysis delivered very clear results confirming the admixed origin of A. sachalinensis, with a genetic contribution from A. nephrolepis. No variation in cytoplasmic markers was found in A. gracilis, suggesting the occurrence of a recent bottleneck. Main conclusions There is a clear reduction of genetic diversity in Abies species from the Pacific coast into the continent. The higher diversity in A. sachalinensis could have two causes: a larger effective population size in the islands due to relatively stable climatic conditions and consequently less pronounced demographic fluctuations in population size and/or hybridization with continental and Japanese populations. Sakhalin Island is a major transitional zone for conifer species. Finally, the fir from Kamchatka, A. gracilis, should be regarded as a separate species closely related to the A. nephrolepis-A. sachalinensis complex.

  • 12.
    Seppä, Perttu
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Fogelqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Gyllenstrand, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Lorenzi, M. C.
    Colony kin structure and breeding patterns in the social wasp, Polistes biglumis2011In: Insectes Sociaux, ISSN 0020-1812, E-ISSN 1420-9098, Vol. 58, no 3, p. 345-355Article in journal (Refereed)
    Abstract [en]

    We used DNA microsatellites to study colony kin structure and breeding patterns in the primitively eusocial wasp Polistes biglumis. P. biglumis inhabits cool areas at high altitudes and, as a consequence, has a reduced colony cycle compared to more temperate Polistes. P. biglumis colonies are always founded and controlled by a single foundress, but nest failure is common and foundresses losing their nests do not have time to start new ones due to the short season. Instead, nests are characterized by frequent female turnover, in the form of females taking over (usurpation) other con-specific nests. Our results showed that most nests had offspring from multiple unrelated females, including some where multiple females were not observed in monitoring. Reconstruction of behavioural events from the genetic data revealed three types of multiple matriline nests: (a) nests that were usurped by another female, where the original nest owner disappeared following the usurpation event, (b) nests that were joined by another female, where the original nest owner stayed following the joining event, (c) nests that were both usurped and joined by other females. We also found, for the first time, a clear indication of multiple mating by Polistes females. Moreover, males mating with the same female were related, which may be explained by the lek mating system of P. biglumis. Finally, we analysed the nest sex ratios and how it changed during the season and found that sexes were produced sequentially, males before females.

  • 13. Shoda-Kagaya, E.
    et al.
    Saito, S.
    Okada, M.
    Nozaki, A.
    Nunokawa, K.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Genetic structure of the oak wilt vector beetle Platypus quercivorus: inferences toward the process of damaged area expansion2010In: BMC Ecology, ISSN 1472-6785, E-ISSN 1472-6785, Vol. 10, no 21Article in journal (Refereed)
  • 14.
    Sjödin, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Hedman, Harald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Shavorskaya, O.
    Finet, Cédric
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Recent degeneration of an old duplicated flowering time gene in Brassica nigra2007In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 98, no 6, p. 375-384Article in journal (Refereed)
    Abstract [en]

    Gene and genome duplications play a major role in the evolution of plant species. The Brassica nigra genome is highly replicated as a result of ancient polyploidization events. Two copies of the flowering time gene CONSTANS (COa and COb) have been identified in B. nigra, and previous studies showed that COa is functional. In the present study, the polymorphism of 92 COb alleles sampled in seven populations was analyzed. Both polymorphism and recombination levels were elevated and varied strongly among populations and 8% of COb alleles exhibit apparently disabling mutations. Sequence data, however, do not provide unambiguous support for the presence of relaxed selective constraint on COb as compared to known functional CO genes. On the one hand, some of the disabling mutations reached high-frequency arguing for a loss of function but, on the other hand, the ratio of nonsynonymous to synonymous nucleotide polymorphism and diversity is low and similar to that observed in other B. nigra CO and CO-like genes, supporting the conservation of some function. We also showed that COb is still transcribed. Finally, the flowering time of Arabidopsis thaliana co mutant plants transformed with COb alleles with and without apparent disabling mutations was similar. We propose that COb was retained for a long period after duplication, but a recent fixation of a detrimental mutation, possibly as an effect of a bottleneck, resulted in its nonfunctionalization. We also speculate as to the presence of subsequent selection for rapid degeneration of the gene.

  • 15.
    Slotte, Tanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Foxe, John Paul
    Hazzouri, Khaled Michel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wright, Stephen I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Genome-Wide Evidence for Efficient Positive and Purifying Selection in Capsella grandiflora, a Plant Species with a Large Effective Population Size2010In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 8, p. 1813-1821Article in journal (Refereed)
    Abstract [en]

    Recent studies comparing genome-wide polymorphism and divergence in Drosophila have found evidence for a surprisingly high proportion of adaptive amino acid fixations, but results for other taxa are mixed. In particular, few studies have found convincing evidence for adaptive amino acid substitution in plants. To assess the generality of this finding, we have sequenced 257 loci in the outcrossing crucifer Capsella grandiflora, which has a large effective population size and low population structure. Using a new method that jointly infers selective and demographic effects, we estimate that 40% of amino acid substitutions were fixed by positive selection in this species, and we also infer a low proportion of slightly deleterious amino acid mutations. We contrast these estimates with those for a similar data set from the closely related Arabidopsis thaliana and find significantly higher rates of adaptive evolution and fewer nearly neutral mutations in C. grandiflora. In agreement with results for other taxa, genes involved in reproduction show the strongest evidence for positive selection in C. grandiflora. Taken together, these results imply that both positive and purifying selection are more effective in C. grandiflora than in A. thaliana, consistent with the contrasting demographic history and effective population sizes of these species.

  • 16.
    St.Onge, Kate
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Demography and Polyploidy in Capsella2010Doctoral 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.

    List of papers
    1. Splicing variation at a FLOWERING LOCUS C homeolog is associated with flowering time variation in the tetraploid Capsella bursa-pastoris
    Open this publication in new window or tab >>Splicing variation at a FLOWERING LOCUS C homeolog is associated with flowering time variation in the tetraploid Capsella bursa-pastoris
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    2009 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 183, no 1, p. 337-345Article in journal (Refereed) Published
    Abstract [en]

    The long-term fates of duplicate genes are well studied both empirically and theoretically, but how the short-term evolution of duplicate genes contributes to phenotypic variation is less well known. Here, we have studied the genetic basis of flowering time variation in the disomic tetraploid Capsella bursa-pastoris. We sequenced four duplicate candidate genes for flowering time and 10 background loci in samples from western Eurasia and China. Using a mixed-model approach that accounts for population structure, we found that polymorphisms at one homeolog of two candidate genes, FLOWERING LOCUS C (FLC) and CRYPTOCHROME1 (CRY1), were associated with natural flowering time variation. No potentially causative polymorphisms were found in the coding region of CRY1; however, at FLC two splice site polymorphisms were associated with early flowering. Accessions harboring nonconsensus splice sites expressed an alternatively spliced transcript or did not express this FLC homeolog. Our results are consistent with the function of FLC as a major repressor of flowering in Arabidopsis thaliana and imply that nonfunctionalization of duplicate genes could provide an important source of phenotypic variation.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-114084 (URN)10.1534/genetics.109.103705 (DOI)000272067000030 ()19581451 (PubMedID)
    Available from: 2010-02-09 Created: 2010-02-09 Last updated: 2017-12-12
    2. Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems
    Open this publication in new window or tab >>Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems
    Show others...
    2011 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 16, p. 3306-3320Article in journal (Refereed) Published
    Abstract [en]

    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.

     

    Keywords
    selfing, Brassicaceae, genetic structure, genetic diversity
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-136767 (URN)10.1111/j.1365-294X.2011.05189.x (DOI)000293750000003 ()
    Available from: 2010-12-14 Created: 2010-12-14 Last updated: 2017-12-11Bibliographically approved
    3. The impact of sampling schemes on demographic inference: an empirical study in two species with different mating systems and demographic histories
    Open this publication in new window or tab >>The impact of sampling schemes on demographic inference: an empirical study in two species with different mating systems and demographic histories
    2012 (English)In: G3-Genes Genomes Genetics, ISSN 2160-1836, Vol. 2, no 7, p. 803-814Article in journal (Refereed) Published
    Abstract [en]

    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.

     

    Keywords
    population structure, Tajima’s D, frequency spectrum, Capsella
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-136784 (URN)10.1534/g3.112.002410 (DOI)000312454800009 ()
    Available from: 2010-12-14 Created: 2010-12-14 Last updated: 2013-01-21Bibliographically approved
    4. Coalescent-based analysis distinguishes between allo- and autopolyploid origin in shepherd’s purse (Capsella bursa-pastoris)
    Open this publication in new window or tab >>Coalescent-based analysis distinguishes between allo- and autopolyploid origin in shepherd’s purse (Capsella bursa-pastoris)
    Show others...
    2012 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 7, p. 1721-1733Article 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.

    Keywords
    autopoplyploidy, coalescent, Brassicaceae, Approximate bayesian computation, IM model
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-136786 (URN)10.1093/molbev/mss024 (DOI)000305409000004 ()
    Note

    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: 2017-12-11
  • 17.
    St.Onge, Kate
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Tanja, Slotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Palmé, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 16, p. 3306-3320Article in journal (Refereed)
    Abstract [en]

    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.

     

  • 18.
    St.Onge, Kate
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Palmé, Anna E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Wright, Stephen I.
    Department of Ecology and Evolutionary Biology, University of Toronto.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The impact of sampling schemes on demographic inference: an empirical study in two species with different mating systems and demographic histories2012In: G3-Genes Genomes Genetics, ISSN 2160-1836, Vol. 2, no 7, p. 803-814Article in journal (Refereed)
    Abstract [en]

    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.

     

  • 19. Stutz, Silvina
    et al.
    Marcela Borel, C.
    Fontana, Sonia L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    del Puerto, Laura
    Inda, Hugo
    Garcia-Rodriguez, Felipe
    Tonello, Marcela S.
    Late Holocene climate and environment of the SE Pampa grasslands, Argentina, inferred from biological indicators in shallow, freshwater Lake Nahuel Rucá2010In: Journal of Paleolimnology, ISSN 0921-2728, E-ISSN 1573-0417, Vol. 44, no 3, p. 761-775Article in journal (Refereed)
    Abstract [en]

    We analyzed pollen, non-pollen palynomorphs (NPPs), calcareous microfossils, plant macrofossils, diatoms, chrysophyte cysts, opal phytoliths and organic matter content in a 123-cm sediment sequence from Nahuel Ruca Lake, a shallow, freshwater system in the southeastern Pampa grasslands, Argentina. Three stages in the lake evolution were identified. Before 3,680 cal year BP, only pollen, NPPs (dinoflagellate cysts and acritarchs) and ostracods were recovered, suggesting brackish/saline conditions in the lake and nearby areas. Freshwater conditions are, however, indicated by Myriophyllum, Pediastrum and Zygnemataceae. The brackish/saline conditions could have been caused by marine influence during a Holocene sea level high stand that affected the area ca. 6,000 year BP. Between 3,680 and 390 cal year BP, macrophyte pollen and plant macrofossils indicate increasingly freshwater conditions in the lake and the adjacent area. Diatom and ostracod assemblages, however, suggest brackish and oligotrophic conditions, giving way to freshwater and meso-eutrophic conditions toward the end of this period. The relationship between submersed macrophytes (Myriophyllum, Potamogeton, Ceratophyllum, Chara) and planktonic algae (Chlorophyta and diatoms), suggests a shift in the lake from a clear to a turbid state. This turbid state is more evident after 390 cal year BP. High values of Pediastrum, Scenedesmus and diatoms (Cyclotella meneghiniana, Aulacoseira granulata, A. muzzanensis) observed during this stage could have reduced light penetration, with consequent loss of submersed plants. Pollen and plant macrofossils in the uppermost 20 cm indicate a shallow, freshwater lake similar to present, though an increase in brackish/freshwater diatoms suggests an increase in salinity, perhaps related to periodic droughts. Opal phytoliths yield a regional paleoclimatic reconstruction that agrees closely with inferences made using pollen, mammals and sediment characteristics.

  • 20. Thorsson, A. E. Th.
    et al.
    Palsson, S.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Anamthawat-Jonsson, K.
    Introgression and phylogeography of Betula nana (diploid), B-pubescens (tetraploid) and their triploid hybrids in Iceland inferred from cpDNA haplotype variation2010In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, no 11, p. 2098-2110Article in journal (Refereed)
    Abstract [en]

    Aim The objective was to find direct genetic evidence supporting introgressive hybridization between tetraploid tree birch (Betula pubescens) and diploid dwarf birch (B. nana), via triploid hybrids, and to investigate an association between the introgression and phylogeographical distribution of Icelandic birch. Location Samples were collected from 463 trees in 12 woodlands in Iceland and eight locations in Norway, Sweden, Scotland and Greenland. Methods Ploidy status of individual trees was determined by chromosome counting. Variation in the chloroplast genome was assessed using polymerase chain reaction-restriction fragment length polymorphism. The geographical distribution of the haplotypes was mapped. The haplotype variation and introgression ratios (IG) were analysed statistically. Results Thirteen haplotypes were identified among Icelandic samples. The most common haplotype (T, 49% occurrence) was present in all ploidy groups and in all woodlands. All common haplotypes were shared between the triploid group and the parental species, indicating introgressive hybridization. This was supported by the statistical analysis of IG indices and the variation components. Considerable differences existed among samples, shaped by isolation by distance and local introgression. An east-west phylogeographical distribution in Iceland was observed. Main conclusions Despite extensive introgression across species and ploidy levels, a biogeographical pattern has been observed, and this may indicate different population histories or multiple origins of Icelandic birch. The chloroplast haplotype diversity found in Iceland resembles that found in birch populations from northern Scandinavia.

  • 21.
    Tsuda, Yoshiaki
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Ide, Yuji
    Chloroplast DNA phylogeography of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in Japan2010In: Journal of plant research, ISSN 0918-9440, E-ISSN 1618-0860, Vol. 123, no 3, p. 343-353Article in journal (Refereed)
    Abstract [en]

    Betula maximowicziana is an ecologically and economically important tree species in Japan. In order to examine the phylogeographical pattern of the species in detail, maternally inherited chloroplast (cp) DNA variations of 25 natural populations of Betula maximowicziana and a total of 12 populations of three related species were evaluated by PCR-RFLP analysis. Two main haplotypic groups of B. maximowicziana populations (northern and southern) were detected, with the main boundary passing through the Tohoku region in northeastern Japan; in addition there was high genetic differentiation among the 25 populations studied (G (ST) = 0.950, [Formula: see text]). The phylogeographical pattern exhibited by B. maximowicziana was much more similar to that of alpine plants than to that of beech and oak. Comparison of the patterns of genetic structure obtained from the cpDNA with previously and newly acquired data on bi-parentally inherited nuclear DNA indicates that the nuclear genome was transferred via pollen from the northern haplotypic group to the southern group more frequently than it moved in the opposite direction. Although common haplotypes were detected among B. maximowicziana and the two related species examined, these haplotypes were not shared sympatrically, suggesting very rare hybridization among the species currently occurring in their natural populations.

  • 22.
    Tsuda, Yoshiaki
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Sawada, Haruo
    Ohsawa, Takafumi
    Nakao, Katsuhiro
    Nishikawa, Hiroki
    Ide, Yuji
    Landscape genetic structure of Betula maximowicziana in the Chichibu mountain range, central Japan2010In: Tree Genetics and Genomes, ISSN 1614-2942, Vol. 6, no 3, p. 377-387Article in journal (Refereed)
    Abstract [en]

    We evaluated the genetic structure of 16 Betula maximowicziana populations in the Chichibu mountain range, central Japan, located within a 25-km radius; all but two populations were at altitudes of 1,100–1,400 m. The results indicate the effects of geographic topology on the landscape genetic structure of the populations and should facilitate the development of local-scale strategies to conserve and manage them. Analyses involving 11 nuclear simple sequence repeat loci showed that most populations had similar intrapopulation genetic diversity parameters. Population differentiation (F ST = 0.021, G′ST = 0.033) parameters for the populations examined were low but were relatively high compared to those obtained in a previous study covering populations in a much larger area with a radius of approximately 1,000 km (F ST = 0.062, G′ST = 0.102). Three populations (Iriyama, Kanayamasawa, and Nishizawa) were differentiated from the other populations by Monmonier’s and spatial analysis of molecular variance algorithms or by STRUCTURE analysis. Since a high mountain ridge (nearly 2,000 m) separates the Kanayamasawa and Nishizawa populations from the other 14 populations and the Kanayamasawa and Nishizawa populations are themselves separated by another mountain ridge, the genetic structure appears to be partly due to mountain ridges acting as genetic barriers and restricting gene flow. However, the Iriyama population is genetically different but not separated by any clear geographic barrier. These results show that the landscape genetic structure is complex in the mountain range and we need to pay attention, within landscape genetic studies and conservation programs, to geographic barriers and local population differentiation.

1 - 22 of 22
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