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  • 1. Alström-Rapaport, Cecilia
    et al.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Wallén, Johan
    Lascoux, Martin
    Phylogeographic structure in Brassica nigra, a signal of early agricultural spread in Europe?Manuscript (Other (popular science, discussion, etc.))
  • 2. An, Junghwa
    et al.
    Bechet, Arnaud
    Berggren, Åsa
    Brown, Sarah K.
    Bruford, Michael W.
    Cai, Qingui
    Cassel-Lundhagen, Anna
    Cezilly, Frank
    Chen, Song-Lin
    Cheng, Wei
    Choi, Sung-Kyoung
    Ding, X.Y.
    Fan, Yong
    Feldheim, Kevin A.
    Feng, Z.Y.
    Friesen, Vicki L.
    Gaillard, Maria
    Galaraza, Juan A.
    Gallo, Leonardo
    Ganeshaiah, K. N.
    Geraci, Julia
    Gibbons, John G.
    Grant, William S.
    Grauvogel, Zac
    Gustafsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Guyon, Jeffrey R.
    Han, L.
    Heath, Daniel D.
    Hemmilä, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Hogan, Derek
    Hou, B. W.
    Jakse, Jernej
    Javornik, Branka
    Kanuch, Peter
    Kim, Kyung-Kil
    Kim, Kyung-Seok
    Kim, Sang-Gyu
    Kim, Sang-In
    Kim, Woo-Jin
    Kim, Yi-Kyung
    Klich, Maren A.
    Kreiser, Brian R.
    Kwan, Ye-Seul
    Lam, Athena W.
    Lasater, Kelly
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Lee, Hang
    Lee, Yun-Sun
    Li, D. L.
    Li, Shao-Jing
    Li, W. Y.
    Liao, Xiaolin
    Liber, Zlatko
    Lin, Lin
    Liu, Shaoying
    Luo, Xin-Hui
    Ma, Y. H.
    Ma, Yajun
    Marchelli, Paula
    Min, Mi-Sook
    Moccia, Maria Domenica
    Mohana, Kumara P.
    Moore, Marcelle
    Morris-Pocock, James A.
    Park, Han-Chan
    Pfunder, Monika
    Ivan, Radosavljevic
    Ravikanth, G.
    Roderick, George K.
    Rokas, Antonis
    Sacks, Benjamin N.
    Saski, Christopher A.
    Satovic, Zlatko
    Schoville, Sean D.
    Sebastiani, Federico
    Sha, Zhen-Xia
    Shin, Eun-Ha
    Soliani, Carolina
    Sreejayan, N.
    Sun, Zhengxin
    Tao, Yong
    Taylor, Scott A.
    Templin, William D.
    Shaanker, R. Uma
    Vasudeva, R.
    Vendramin, Giovanni G.
    Walter, Ryan P.
    Wang, Gui-Zhong
    Wang, Ke-Jian
    Wang, Y. Q.
    Wattier, Rémi A.
    Wei, Fuwen
    Widmer, Alex
    Woltmann, Stefan
    Won, Yong-Jin
    Wu, Jing
    Xie, M. L.
    Xu, Genbo
    Xu, Xiao-Jun
    Ye, Hai-Hui
    Zhan, Xiangjiang
    Zhang, F.
    Zhong, J.
    Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 20092010In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 10, no 2, p. 404-408Article in journal (Refereed)
    Abstract [en]

    This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.

  • 3.
    Andersson, Anna-Carin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Alström-Rapaport, Cecilia
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Fredga, Karl
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Lack of mitochondrial DNA divergence between chromosome races of the common shrew, Sorex araneus, in Sweden. Implications for interpreting chromosomal evolution and colonization history.2005In: Mol Ecol, ISSN 0962-1083, Vol. 14, no 9, p. 2703-16Article in journal (Refereed)
  • 4.
    Andersson, Anna-Carin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Narain, Y
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Tegelström, H
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Fredga, K
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    No apparent reduction of gene flow in a hybrid zone between the West and North European karyotypic groups of the common shrew, Sorex araneus.2004In: Mol Ecol, ISSN 0962-1083, Vol. 13, no 5, p. 1205-15Article in journal (Refereed)
    Abstract [en]

    The common shrew, Sorex araneus, exhibits an unusually high level of karyotypic variation. Populations with identical or similar karyotypes are defined as chromosome races, which are, in turn, grouped into larger evolutionary units, karyotypic groups. Using six microsatellite markers, we investigated the genetic structure of a hybrid zone between the Sidensjo and Abisko chromosome races, representatives of two distinct karyotypic groups believed to have been separated during the last glacial maximum, the West European karyotypic group (western group) and the North European karyotypic group (northern group), respectively. Significant FST values among populations suggest some weak genetic structure. All hierarchical levels show similar levels of genetic differentiation, equivalent to levels of genetic structure in several intraracial studies of common shrew populations from central Europe. Notably, genetic differentiation was of the same order of magnitude between and within karyotypic groups. Although the genetic differentiation was weak, the correlation between genetic and geographical distance was positive and significant, suggesting that the genetic variation observed between populations is a function of geographical distance rather than racial origin. Hence, considerable chromosomal differences do not seem to prevent extensive gene flow.

  • 5.
    Andersson, Anna-Carin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Thulin, CG
    Tegelstrom, H
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Applicability of rabbit microsatellite primers for studies of hybridisation between an introduced and a native hare species1999In: HEREDITAS, ISSN 0018-0661, Vol. 130, no 3, p. 309-315Article in journal (Refereed)
    Abstract [en]

    Introduced species may hybridise with relatives in the native Fauna or flora and thereby compete for matings and transmit alien DNA. Such interference may contaminate unique genepools, disturb existing ecological balances and may ultimately result in the

  • 6. Axeisson, T
    et al.
    Shavorskaya, O
    Lagercrantz, U
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Multiple flowering time QTLs within several Brassica species could be the result of duplicated copies of one ancestral gene.2001In: Genome, ISSN 0831-2796, Vol. 44, no 5, p. 856-64Article in journal (Refereed)
  • 7.
    Axelsson, T
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Bowman, C M
    Sharpe, A G
    Lydiate, D J
    Lagercrantz, U
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Amphidiploid Brassica juncea contains conserved progenitor genomes.2000In: Genome, ISSN 0831-2796, Vol. 43, no 4, p. 679-88Article in journal (Refereed)
  • 8.
    Bennett, Keith D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Parducci, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    DNA from pollen: principles and potential2006In: The Holocene, ISSN 0959-6836, E-ISSN 1477-0911, Vol. 16, no 8, p. 1031-1034Article in journal (Refereed)
    Abstract [en]

    This paper describes our recent extraction of ancient DNA (aDNA) from Holocene pollen and discusses the potential of the technique for elucidating timescales of evolutionary change. We show that plastid DNA is recoverable and usable from pollen grains of Scots pine Pinus sylvestris from 10 ka and 100 years ago. Comparison of the ancient sequences with modern sequences, obtained from an extant population, establish a first genetic link between modern and fossil samples of Scots pine, providing a genetic continuity through time. One common haplotype is present in each of the three periods investigated, suggesting that it persisted near the lake throughout the postglacial. The retrieval of aDNA from pollen has major implications for palaeoecology by allowing (i) investigation of population-level dynamics in time and space, and (ii) tracing ancestry of populations and developing phylogenetic trees that include extinct as well as extant taxa. The method should work over the last glacial oscillation, thus giving access to ancestry of populations over a crucial period of time for the understanding of the relationship between speciation and climate change.

  • 9.
    Berg, LM
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Lascoux, M
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Neutral genetic differentiation in an island model with cyclical parthenogenesis2000In: JOURNAL OF EVOLUTIONARY BIOLOGY, ISSN 1010-061X, Vol. 13, no 3, p. 488-494Article in journal (Refereed)
    Abstract [en]

    Unusually high levels of genetic differentiation are often observed between populations of Daphnia (Crustacea: Cladocera) and other cladocerans. Selection and departure from migration-mutation-drift equilibrium have been invoked to explain this fact. Howe

  • 10.
    Berg, LM
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. CONSERVATION BIOLOGY AND GENETICS.
    Lascoux, M
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Pamilo, P
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    The infinite island model with sex-differentiated gene flow1998In: HEREDITY, ISSN 0018-067X, Vol. 81, p. 63-68Article in journal (Refereed)
    Abstract [en]

    Identity measures are derived for the infinite island model with separate sexes and sex-differentiated contribution to gene flow. The concept of effective migration rate, m(e), is introduced, which describes the genetically effective flow when sexes migra

  • 11.
    Berg, LM
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. CONSERVATION BIOLOGY AND GENETICS.
    Palsson, S
    Lascoux, M
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Fitness and sexual response to population density in Daphnia pulex2001In: FRESHWATER BIOLOGY, ISSN 0046-5070, Vol. 46, no 5, p. 667-677Article in journal (Refereed)
    Abstract [en]

    1. The switch between asexual and sexual reproduction is an important fitness component in cyclically parthenogenetic populations as it is the key to persistence in unstable habitats and because it influences population genetic characteristics such as lin

  • 12.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Area-sensitivity of the sand lizard and spider wasps in sandy pine heath forests – umbrella species for early successional biodiversity conservation?2004In: Ecological Bulletins, Vol. 51, p. 189-207Article in journal (Refereed)
  • 13.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Demography and management of relict sand lizard (Lacerta agilis) populations on the edge of extinction2000In: Ecological Bulletins, ISSN 0346-6868, Vol. 48, p. 123-142Article in journal (Refereed)
  • 14.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Habitat tracking and population dynamics of an early successional lizard in a changing pine forest landscapeManuscript (Other (popular science, discussion, etc.))
  • 15.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Population Dynamics and Conservation of the Sand Lizard (Lacerta agilis) on the Edge of its Range2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The sand lizard (Lacerta agilis) reaches the northern periphery of its distribution in south-central Sweden, where small, isolated relict populations occur in pine heath forests on sandy sediments. Modern forestry and fire suppression have reduced the amount of suitable open habitat for the species in this area and seem to be important for its decline. Main objectives of this thesis were to evaluate the efficiency of different management strategies, and if the sand lizard can function as an umbrella species for biodiversity conservation.

    Over a 16-year period, the estimated annual numbers of adult females in each of two study populations fluctuated between 23 and 3. Simulations of stochastic future population growth showed that the risk of extinction was highly dependent on population growth rate, which in turn was strongly affected by juvenile survival as indicated by elasticity analysis.

    Simulations of population growth for 50 years showed that the quasi-extinction risk (threshold ≤ 10 females) was > 56% for patches ≤ 1 ha; which is the observed average size of suitable habitat for inhabited patches during a 10-year period. In managed metapopulation networks with highly co-fluctuating local populations, among-population dispersal was not important to reduce extinction risks over a 50-year horizon.

    In the field the preferred microhabitat of sand lizards was successfully restored using tree felling and patch-soil scarification. The lizards gradually colonized the restored patches, and 16 years after restoration, sand lizards where mainly found there.

    Pine-heath area, and patch area within individual pine heaths, were of major importance for long-term population persistence at regional and landscape scales, respectively. Analyses of nested species subsets and an umbrella index suggest that the sand lizard can be a useful cross-taxonomic umbrella species on both scales for other red-listed species.

    List of papers
    1. Demography and management of relict sand lizard (Lacerta agilis) populations on the edge of extinction
    Open this publication in new window or tab >>Demography and management of relict sand lizard (Lacerta agilis) populations on the edge of extinction
    2000 (English)In: Ecological Bulletins, ISSN 0346-6868, Vol. 48, p. 123-142Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92922 (URN)
    Available from: 2005-04-22 Created: 2005-04-22 Last updated: 2009-04-01Bibliographically approved
    2. Sand lizard (Lacerta agilis) in Central Sweden: Modeling Juvenile Reintroduction and Spatial management Strategies for Metapopulation Establishment
    Open this publication in new window or tab >>Sand lizard (Lacerta agilis) in Central Sweden: Modeling Juvenile Reintroduction and Spatial management Strategies for Metapopulation Establishment
    2004 (English)In: Species Conservation and Management: Case Studies, 2004, p. 326-339Chapter in book (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-92923 (URN)0-19-516646-9 (ISBN)
    Available from: 2005-04-22 Created: 2005-04-22 Last updated: 2009-04-01Bibliographically approved
    3. Habitat tracking and population dynamics of an early successional lizard in a changing pine forest landscape
    Open this publication in new window or tab >>Habitat tracking and population dynamics of an early successional lizard in a changing pine forest landscape
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92924 (URN)
    Available from: 2005-04-22 Created: 2005-04-22 Last updated: 2010-01-14Bibliographically approved
    4. Area-sensitivity of the sand lizard and spider wasps in sandy pine heath forests – umbrella species for early successional biodiversity conservation?
    Open this publication in new window or tab >>Area-sensitivity of the sand lizard and spider wasps in sandy pine heath forests – umbrella species for early successional biodiversity conservation?
    2004 (English)In: Ecological Bulletins, Vol. 51, p. 189-207Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92925 (URN)
    Available from: 2005-04-22 Created: 2005-04-22 Last updated: 2009-04-01Bibliographically approved
  • 16.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Sand lizard (Lacerta agilis) in Central Sweden: Modeling Juvenile Reintroduction and Spatial management Strategies for Metapopulation Establishment2004In: Species Conservation and Management: Case Studies, 2004, p. 326-339Chapter in book (Other academic)
  • 17.
    Bodare, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conservation Genetics and Speciation in Asian Forest Trees2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Tropical forests are important because they are the home of millions of species at the same time as they perform ecosystem services and provide food, cash income and raw materials for the people living there. The present thesis elucidates questions relevant to the conservation of selected forest trees as it adds to the knowledge in the phylogeny, population structure, genetic diversity and adaptation in these species.

    We investigated the genetic diversity and speciation of four spruce species around the Qinghai-Tibetan Plateau (QTP), Western China, and one from Taiwan. Nucleotide diversity was low in P. schrenkiana and the Taiwanese P. morrisonicola but higher in P. likiangensis, P. purpurea and P. wilsonii. This can be explained by the population bottlenecks that were detected in the two former species by coalescent-based analysis. The phylogenetic relationships between the five species were difficult to interpret, possibly because other Asian spruce species might have been involved. However, all species are distinct except P. purpurea, which likely has a hybrid origin. 

    The rate of bud set and expression of the FTL2 gene in response to photoperiod in the southernmost growing spruce species, P. morrisonicola, was studied. We found that in this species, although growing near the equator, bud set appears to be induced mainly by a shortening of photoperiod, similarly to its more northerly growing spruce relatives. In addition, seedlings originating from mother trees growing at higher elevations showed a trend towards earlier bud set than seedlings originating from mother trees at lower altitudes.

    We also studied the population structure and genetic diversity in the endemic white cedar (Dysoxylum malabaricum) in the Western Ghats, India. Overall, no increase in inbreeding that could be related to human activities could be detected. Populations appear to have maintained genetic diversity and gene flow in spite of forest fragmentation over the distribution range. However, there is a severe lack of juveniles and young adults in several populations that needs to be further addressed. Finally, we recommend conservation units based on population structure.

    List of papers
    1. Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Open this publication in new window or tab >>Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Show others...
    2010 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 5, p. 1001-1014Article in journal (Refereed) Published
    Abstract [en]

    Nucleotide variation at 12 to 16 nuclear loci was studied in three spruce species from the Qinghai-Tibetan Plateau (QTP), Picea likiangensis, P. wilsonii and P. purpurea, and one species from the Tian Shan mountain range, P. schrenkiana. Silent nucleotide diversity was limited in P. schrenkiana and high in the three species from the QTP, with values higher than in boreal spruce species, despite their much more restricted distributions compared to that of the boreal species. In contrast to European boreal species that have experienced severe bottlenecks in the past, coalescent-based analysis suggests that DNA polymorphism in the species from the QTP and adjacent areas is compatible with the standard neutral model (P. likiangensis, P. wilsonii, P. schrenkiana) or with population growth (P. purpurea). In order to test if P. purpurea is a diploid hybrid of P. likiangensis and P. wilsonii, we used a combination of approaches, including model based inference of population structure, Isolation-with-Migration models and recent theoretical results on the effect of introgression on the geographic distribution of diversity. In contrast to the three other species, each of which was predominantly assigned to a single cluster in the Structure analysis, P. purpurea individuals were scattered over the three main clusters and not, as we had expected, confined to the P. likiangensis and P. wilsonii clusters. Furthermore the contribution of P. schrenkiana was by far the largest one. In agreement with this, the divergence between P. purpurea and P. schrenkiana was lower than the divergence of either P. likiangensis or P. wilsonii from P. schrenkiana. These results, together with previous ones showing that P. purpurea and P. wilsonii share the same haplotypes at both chloroplast and mitochondrial markers, suggest that P. purpurea has a complex origin, possibly involving additional species.

    Keywords
    Picea, Qinghai Tibetan Plateau, effective population size, divergence time, introgression, speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121399 (URN)10.1093/molbev/msp301 (DOI)000276994800004 ()20031927 (PubMedID)
    Available from: 2010-03-23 Created: 2010-03-23 Last updated: 2017-12-12Bibliographically approved
    2. Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)
    Open this publication in new window or tab >>Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)
    2013 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, p. 3320-3333Article in journal (Refereed) Published
    Abstract [en]

    Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.

    National Category
    Natural Sciences Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198100 (URN)10.1002/ece3.698 (DOI)000324932600011 ()
    Note

    De två (2) första författarna delar förstaförfattarskapet.

    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2017-12-06Bibliographically approved
    3. Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)
    Open this publication in new window or tab >>Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)
    (English)Manuscript (preprint) (Other academic)
    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198107 (URN)
    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2013-08-30
    4. Genetic structure and demographic history of the endangered tree species, Dysoxylum  malabaricum (Meliaceae) in Western Ghats, India: Implications for conservation in a  biodiversity hotspot
    Open this publication in new window or tab >>Genetic structure and demographic history of the endangered tree species, Dysoxylum  malabaricum (Meliaceae) in Western Ghats, India: Implications for conservation in a  biodiversity hotspot
    Show others...
    2013 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, p. 3233-3248Article in journal (Other academic) Published
    Abstract [en]

    The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylummalabaricum (white cedar) is an economically important tree species, endemic to theWestern Ghats, India, one of the world's eight most important biodiversity hotspots. As D.malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-widegenetic structure of twelve D.malabaricum populations was evaluated to assess the impact ofhuman activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (F-IS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred beforethe last glacial maximum. Finally we discussed the implications of these results, in particularthe presence of a clear pattern of historical genetic subdivision, on conservation policies.

    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198109 (URN)10.1002/ece3.669 (DOI)000324932600004 ()
    Note

    De två (2) första författarna delar förstaförfattarskapet.

    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2017-12-06Bibliographically approved
    5. Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, India
    Open this publication in new window or tab >>Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, India
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    Conservation genetics, Dysoxylum malabaricum, fragmentation, land use, spatial genetic structure, Western Ghats
    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-198700 (URN)
    Funder
    Sida - Swedish International Development Cooperation Agency
    Available from: 2013-04-23 Created: 2013-04-23 Last updated: 2013-08-30
  • 18.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)Manuscript (preprint) (Other academic)
  • 19.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ravikanth, G
    Ashoka Trust for Research in Ecology and the Environment.
    Sascha A, Ismail
    Department of Environmental Systems Science, ETH Zürich.
    Kumara Patel, Mohana
    University of Agricultural Sciences, Bangalore .
    Spanu, Ilaria
    Plant Genetics Institute National Research Council.
    Vasudeva, R
    Dharwad College of Forestry, Campus Karnataka .
    Uma Shaanker, R
    Ashoka Trust for Research in Ecology and the Environment.
    Vendramin, Giovanni Giuseppe
    5Plant Genetics Institute National Research Council.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, IndiaManuscript (preprint) (Other academic)
  • 20.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Yang, J-C
    Taiwan Forestry Research Institute.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)2013In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, p. 3320-3333Article in journal (Refereed)
    Abstract [en]

    Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.

  • 21.
    Brg, Lars M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Fluctuating selection, egg banks and population genetic structure in cyclically parthenogenetic species.2005In: Hydrobiologia, Vol. 549, p. 287-295Article in journal (Refereed)
  • 22. Carlsson, Jenny
    et al.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Sundström, Jens
    Teixeira, Rita
    Wellmer, Frank
    Meyerowitz, Elliot M.
    Glimelius, Kristina
    Microarray analysis reveals altered expression of a large number of nuclear genes in developing cytoplasmic male sterile Brassica napus flowers2007In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 49, no 3, p. 452-462Article in journal (Refereed)
    Abstract [en]

    To gain new insights into the mechanism underlying cytoplasmic male sterility (CMS), we compared the nuclear gene expression profiles of flowers of a Brassica napus CMS line with that of the fertile B. napus maintainer line using Arabidopsis thaliana flower-specific cDNA microarrays. The CMS line used has a B. napus nuclear genome, but has a rearranged mitochondrial (mt) genome consisting of both B. napus and A. thaliana DNA. Gene expression profiling revealed that a large number of genes differed in expression between the two lines. For example, nuclear genes coding for proteins that are involved in protein import into organelles, genes expressed in stamens and pollen, as well as genes implicated in either cell-wall remodeling or architecture, were repressed in the CMS line compared with B. napus. These results show that the mt genome of the CMS line strongly influences nuclear gene expression, and thus reveal the importance of retrograde signalling between the mitochondria and the nucleus. Furthermore, flowers of the CMS line are characterized by a replacement of stamens with carpelloid organs, and thus partially resemble the APETALA3 (AP3) and PISTILLATA (PI) mutants. In accordance with this phenotype, AP3 expression was downregulated in the stamens, shortly before these organs developed carpelloid characteristics, even though it was initiated correctly. Repression of PI succeeded that of AP3 and might be a consequence of a loss of AP3 activity. These results suggest that AP3 expression in stamens depends on proper mt function and a correct nuclear-mt interaction, and that mt alterations cause the male sterility phenotype of the CMS line.

  • 23. Ceplitis, Alf
    et al.
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Neuffer, Barbara
    Linde, Marcus
    Kraft, Thomas
    Lascoux, Martin
    QTL mapping of flowering time using AFLP and candidate gene markers in the tetraploid Capsella bursa-pastoris (Brassicaceae).Manuscript (Other (popular science, discussion, etc.))
  • 24.
    Ceplitis, Alf
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Su, Yingtao
    Lascoux, Martin
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae).2005In: Mol Ecol, ISSN 0962-1083, Vol. 14, no 14, p. 4221-33Article in journal (Other scientific)
  • 25.
    Chen, J
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Kallman, T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Gyllenstrand, N
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Lascoux, M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict2010In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 104, no 1, p. 3-14Article in journal (Refereed)
    Abstract [en]

    In all, 10 nuclear loci were re-sequenced in four spruce species. Three of the species are boreal species with very large natural ranges: Picea mariana and P. glauca are North American, and P. abies, is Eurasian. The fourth species, P. breweriana, is a Tertiary relict from Northern California, with a very small natural range. Although the boreal species population sizes have fluctuated through the Ice Ages, P. breweriana is believed to have had a rather stable population size through the Quaternary. Indeed, the average Tajima’s D was close to zero in this species and negative in the three boreal ones. Reflecting differences in current population sizes, nucleotide diversity was an order of magnitude lower in P. breweriana than in the boreal species. This is in contrast to the similar and high levels of heterozygosity observed in previous studies at allozyme loci across species. As the species have very different histories and effective population sizes, selection at allozyme loci rather than demography appears to be a better explanation for this discrepancy. Parameters of Isolation-with-Migration (IM) models were also estimated for pairs of species. Shared polymorphisms were extensive and fixed polymorphisms few. Divergence times were much shorter than those previously reported. There was also evidence of historical gene flow between P. abies and P. glauca. The latter was more closely related to P. abies than to its sympatric relative P. mariana. This last result suggests that North American and Eurasian species might have been geographically much closer in the recent past than they are today.

  • 26. Das, S
    et al.
    Lagercrantz, Ulf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär Funktionsgenomik.
    Lascoux, Martin
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär Funktionsgenomik.
    Black mustard2006In: Genome mapping and molecular breeding in plants: Oilseeds, Springer, , 2006Chapter in book (Refereed)
  • 27.
    Florin, Ann-Britt
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Gyllenstrand, Niclas
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Isolation and characterization of polymorphic microsatellite markers in the blowflies Lucilia illustris and Lucilia sericata2002In: Molecular Ecology Notes, Vol. 2, p. 113-116Article in journal (Refereed)
  • 28.
    Foster, KR
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Ratnieks, FLW
    Gyllenstrand, N
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Thoren, PA
    Colony kin structure and male production in Dolichovespula wasps2001In: MOLECULAR ECOLOGY, ISSN 0962-1083, Vol. 10, no 4, p. 1003-1010Article in journal (Refereed)
    Abstract [en]

    In annual hymenopteran societies headed by a single outbred queen, paternity (determined by queen mating frequency and sperm use) is the sole variable affecting colony kin structure and is therefore a key predictor of colony reproductive characteristics.

  • 29.
    Fredga, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Reconstruction of postglacial colonization of Sorex araneus into northern Scandinavia based on karyotype studies, and the subdivision of the Abisko race into three2007In: Russian Journal of Theriology, Vol. 6, p. 85-96Article in journal (Refereed)
  • 30.
    Gerber, S
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. CONSERVATION BIOLOGY AND GENETICS.
    Lascoux, M
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Kremer, A
    Relation between protein markers and quantitative traits in maritime pine (Pinus pinaster AIT.)1997In: SILVAE GENETICA, ISSN 0037-5349, Vol. 46, no 5, p. 286-291Article in journal (Refereed)
    Abstract [en]

    Eighteen maritime pines (Pinus pinaster AIT.) were genotyped at 84 loci using 2-dimensional electrophoresis of total protein contained in their haploid megagametophyte. These trees were also characterised for megagametophyte weight and for 49 traits relat

  • 31. Guo, Ya-Long
    et al.
    Bechsgaard, Jesper S
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Neuffer, Barbara
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Weigel, Detlef
    Schierup, Mikkel H
    Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 13, p. 5246-5251Article in journal (Refereed)
    Abstract [en]

    Flowering plants often prevent selfing through mechanisms of self-incompatibility (S.I.). The loss of S.I. has occurred many times independently, because it provides short-term advantages in situations where pollinators or mates are rare. The genus Capsella, which is closely related to Arabidopsis, contains a pair of closely related diploid species, the self-incompatible Capsella grandiflora and the self-compatible Capsella rubella. To elucidate the transition to selfing and its relationship to speciation of C. rubella, we have made use of comparative sequence information. Our analyses indicate that C. rubella separated from C. grandiflora recently ( approximately 30,000-50,000 years ago) and that breakdown of S.I. occurred at approximately the same time. Contrasting the nucleotide diversity patterns of the 2 species, we found that C. rubella has only 1 or 2 alleles at most loci, suggesting that it originated through an extreme population bottleneck. Our data are consistent with diploid speciation by a single, selfing individual, most likely living in Greece. The new species subsequently colonized the Mediterranean by Northern and Southern routes, at a time that also saw the spread of agriculture. The presence of phenotypic diversity within modern C. rubella suggests that this species will be an interesting model to understand divergence and adaptation, starting from very limited standing genetic variation.

  • 32.
    Gustafsson, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Flowering frequency in a small population of Gymnadenia conopsea: a five year study2004In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 24, no 5, p. 599-605Article in journal (Refereed)
    Abstract [en]

    This investigation evaluates the usage of genetic markers, microsatellites, to distinguish and re-identify individual plants in a population of the orchid Gymnadenia conopsea. The study also illustrates the problem in estimating the size of a population from single year sampling as individuals can rest underground or occur in vegetative states; information extremely important for the understanding of population dynamics as well as providing information for conservation management. The total population size was, based on information from microsatellite loci, estimated to 84 individuals and vastly larger than the annual number of flowering plants (mean 31.4 individual s/year). Flowering frequency varied from 24-49%, 53 individuals flowered once, five individuals were flowering four years and a single individual was flowering five years. A common pattern was one or two flowering periods followed by a non-flowering period. The observed number of alleles and the observed and expected heterozygosity varied among loci, although allele frequencies and genotype frequencies did not vary significantly among years.

  • 33.
    Gyllenstrand, N
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Seppä, P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Conservation genetics of the wood ant, Formica lugubris, in a fragmented landscape.2003In: Mol Ecol, ISSN 0962-1083, Vol. 12, no 11, p. 2931-40Article in journal (Other scientific)
  • 34.
    Gyllenstrand, N
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Seppä, P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Pamilo, P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Restricted gene flow between two social forms in the ant Formica truncorum.2005In: J Evol Biol, ISSN 1010-061X, Vol. 18, no 4, p. 978-84Article in journal (Other scientific)
  • 35.
    Gyllenstrand, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Clapham, David
    SLU.
    Källman, Thomas
    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.
    A Norway spruce FLOWERING LOCUS T homolog is implicated in control of growth rhythm in conifers2007In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 144, no 1, p. 248-257Article in journal (Refereed)
    Abstract [en]

    Growth in perennial plants possesses an annual cycle of active growth and dormancy that is controlled by environmental factors, mainly photoperiod and temperature. In conifers and other nonangiosperm species, the molecular mechanisms behind these responses are currently unknown. In Norway spruce (Picea abies L. Karst.) seedlings, growth cessation and bud set are induced by short days and plants from southern latitudes require at least 7 to 10 h of darkness, whereas plants from northern latitudes need only 2 to 3 h of darkness. Bud burst, on the other hand, is almost exclusively controlled by temperature. To test the possible role of Norway spruce FLOWERING LOCUS T (FT)-like genes in growth rhythm, we have studied expression patterns of four Norway spruce FT family genes in two populations with a divergent bud set response under various photoperiodic conditions. Our data show a significant and tight correlation between growth rhythm (both bud set and bud burst), and expression pattern of one of the four Norway spruce phosphatidylethanolamine-binding protein gene family members (PaFT4) over a variety of experimental conditions. This study strongly suggests that one Norway spruce homolog to the FT gene, which controls flowering in angiosperms, is also a key integrator of photoperiodic and thermal signals in the control of growth rhythms in gymnosperms. The data also indicate that the divergent adaptive bud set responses of northern and southern Norway spruce populations, both to photoperiod and light quality, are mediated through PaFT4. These results provide a major advance in our understanding of the molecular control of a major adaptive trait in conifers and a tool for further molecular studies of adaptive variation in plants.

  • 36.
    Gyllenstrand, Niclas
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Gertsch, Pia
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Pamilo, P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Polymorphic microsatellite DNA markers in the ant Formica exsecta2002In: Molecular Ecology Notes, Vol. 2, p. 67-69Article in journal (Refereed)
  • 37.
    Gyllenstrand, Niclas
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Seppä, Perttu
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Pamilol, Pekka
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Genetic differentiation in sympatric wood ants, formica rufa and F.polyctena2004In: Insectes sociaux, Vol. 51, p. 139-145Article in journal (Refereed)
  • 38. Hall, D.
    et al.
    Luquez, V.
    Garcia, V. M.
    St Onge, K. R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Jansson, S.
    Ingvarsson, P. K.
    ADAPTIVE POPULATION DIFFERENTIATIONIN PHENOLOGY ACROSS A LATITUDINALGRADIENT IN EUROPEAN ASPEN (POPULUSTREMULA, L.): A COMPARISON OF NEUTRALMARKERS, CANDIDATE GENES ANDPHENOTYPIC TRAITS2007In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 61, p. 2849-2860Article in journal (Refereed)
  • 39.
    Hedman, Harald
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Källman, Thomas
    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.
    Early evolution of the MFT-like gene family in plants2009In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 70, no 4, p. 359-369Article in journal (Refereed)
    Abstract [en]

    Angiosperm genes sharing a conserved phosphatidylethanolamine-binding (PEPB) domain have been shown to be involved in the control of shoot meristem identity and flowering time. The family is divided into three subfamilies, FT-like, TFL1-like and MFT-like. This study is focused on the evolution of the MFT-like clade, suggested to be ancestral to the two other clades. We report that the bryophyte Physcomitrella patens and the lycopod Selaginella moellendorfii contain four and two MFT-like genes respectively. Neither species have any FT or TFL1-like genes. Furthermore, we have identified a new subclade of MFT-like genes in Angiosperms. Quantitative expression analysis of MFT-like genes in Physcomitrella patens reveals that the expression patterns are circadian and reaches maximum in gametangia and sporophytes. Our data suggest that the occurrence FT and TFL1-like genes, is associated with the evolution of seed plants. Expression data for Physcomitrella MFT-like genes implicates an involvement in the development of reproductive tissues in the moss.

  • 40.
    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.

  • 41.
    Heuertz, Myriam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    De Paoli, Emanuele
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Larsson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Jurman, Irena
    Morgante, Michele
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Gyllenstrand, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]2006In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 174, no 4, p. 2095-2105Article in journal (Refereed)
    Abstract [en]

    DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce [Picea abies (L.) Karst.] haplotypes sampled in seven populations representative of the natural range. The overall nucleotide variation was limited, being lower than that observed in most plant species so far studied. Linkage disequilibrium was also restricted and did not extend beyond a few hundred base pairs. All populations, with the exception of the Romanian population, could be divided into two main domains, a Baltico-Nordic and an Alpine one. Mean Tajima's D and Fay and Wu's H across loci were both negative, indicating the presence of an excess of both rare and high-frequency-derived variants compared to the expected frequency spectrum in a standard neutral model. Multilocus neutrality tests based on D and H led to the rejection of the standard neutral model and exponential growth in the whole population as well as in the two main domains. On the other hand, in all three cases the data are compatible with a severe bottleneck occurring some hundreds of thousands of years ago. Hence, demographic departures from equilibrium expectations and population structure will have to be accounted for when detecting selection at candidate genes and in association mapping studies, respectively.

  • 42.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Studies on Natural Variation and Evolution of Photoperiodism in Plants2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Photoperiodism refers to the organism’s ability to detect and respond to seasonal changes in the daily duration of light and dark and thus constitutes one of the most significant and complex examples of the interaction between the organism and its environment. This thesis attempts to describe the prevalence of variation in a photoperiodic response, its adaptive value, and its putative genetic basis in a common cruciferous weed, Capsella bursa-pastoris (Brassicaceae). Furthermore, the thesis presents a first comprehensive comparative overview of the circadian clock mechanism in an early land plant, Physcomitrella patens (Bryophyta), thus providing insights into the evolution of the plant circadian system.

    In an introductory survey of global gene expression changes among early- and late flowering accessions of C. bursa-pastoris we found an enrichment of genes involved in photoperiodic response and regulation of the circadian clock. Secondly, by phenotyping circadian rhythm variation in a worldwide sample of accessions with known flowering time, we detected robust latitudinal clines in flowering time and circadian period length, which constitute strong indications of local adaptation to photoperiod in the shaping of flowering time variation in this species. In an attempt to elucidate putative genetic causes for the correlated variation between circadian rhythm and flowering time, we found that sequence variation and diverged expression in components regulating light input to the clock, PHYTOCHROME B (PHYB) and DE-ETIOLATED 1 (DET1) make them strong candidate genes. Finally, we present a comparative study of circadian network topology in the moss P. patens. Phylogenetic analyses and time series expression studies of putative clock homologues indicated that several core clock genes present in vascular plants appeared to be lacking in the moss. Consequently, while the clock mechanism in higher plants constitutes at least a three-loop system of interacting components, the moss clock appears to comprise only a single loop.

    We conclude that C. bursa-pastoris is a highly suitable model system for the further elucidation of the molecular variation that influences adaptive change in natural plant populations. Furthermore, we believe that the continuing study of the seemingly less complex circadian network of P. patens not only can provide insights into the evolution of the plant circadian system, but also may help to clarify some of the remaining issues of the circadian clock mechanism in higher plants.

    List of papers
    1. Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae)
    Open this publication in new window or tab >>Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae)
    Show others...
    2007 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 145, no 1, p. 160-173Article, review/survey (Refereed) Published
    Abstract [en]

    Understanding the genetic basis of natural variation is of primary interest for evolutionary studies of adaptation. In Capsella bursa-pastoris, a close relative of Arabidopsis (Arabidopsis thaliana), variation in flowering time is correlated with latitude, suggestive of an adaptation to photoperiod. To identify pathways regulating natural flowering time variation in C. bursa-pastoris, we have studied gene expression differences between two pairs of early- and late-flowering C. bursa-pastoris accessions and compared their response to vernalization. Using Arabidopsis microarrays, we found a large number of significant differences in gene expression between flowering ecotypes. The key flowering time gene FLOWERING LOCUS C (FLC) was not differentially expressed prior to vernalization. This result is in contrast to those in Arabidopsis, where most natural flowering time variation acts through FLC. However, the gibberellin and photoperiodic flowering pathways were significantly enriched for gene expression differences between early- and late-flowering C. bursa-pastoris. Gibberellin biosynthesis genes were downregulated in late-flowering accessions, whereas circadian core genes in the photoperiodic pathway were differentially expressed between early- and late-flowering accessions. Detailed time-series experiments clearly demonstrated that the diurnal rhythm of CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and TIMING OF CAB EXPRESSIONI (TOC1) expression differed between flowering ecotypes, both under constant light and long-day conditions. Differential expression of flowering time genes was biologically validated in an independent pair of flowering ecotypes, suggesting a shared genetic basis or parallel evolution of similar regulatory differences. We conclude that genes involved in regulation of the circadian clock, such as CCA1 and TOC1, are strong candidates for the evolution of adaptive flowering time variation in C. bursa-pastoris.

    Keywords
    Spermatophyta, Angiospermae, Dicotyledones, Cruciferae, Capsella bursa-pastoris, Adaptation, Gene
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96450 (URN)10.1104/pp.107.102632 (DOI)000249285200015 ()
    Available from: 2007-11-15 Created: 2007-11-15 Last updated: 2017-12-14Bibliographically approved
    2. Natural variation in circadian rhythm in a worldwide sample of Capsella bursa-pastoris (Brassicaceae)
    Open this publication in new window or tab >>Natural variation in circadian rhythm in a worldwide sample of Capsella bursa-pastoris (Brassicaceae)
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-119230 (URN)
    Available from: 2010-02-24 Created: 2010-02-24 Last updated: 2010-02-24
    3. Genetic basis for correlated variation in circadian rhythm and flowering time in the tetraploid weed Capsella bursa-pastoris (Brassicaceae)
    Open this publication in new window or tab >>Genetic basis for correlated variation in circadian rhythm and flowering time in the tetraploid weed Capsella bursa-pastoris (Brassicaceae)
    (English)Manuscript (preprint) (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-119232 (URN)
    Available from: 2010-02-24 Created: 2010-02-24 Last updated: 2010-02-24
    4. Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop?
    Open this publication in new window or tab >>Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop?
    Show others...
    2010 (English)In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 10, p. 109-Article in journal (Refereed) Published
    Abstract [en]

    Background: The endogenous circadian clock allows the organism to synchronize processes both to daily and seasonal changes. In plants, many metabolic processes such as photosynthesis, as well as photoperiodic responses, are under the control of a circadian clock. Comparative studies with the moss Physcomitrella patens provide the opportunity to study many aspects of land plant evolution. Here we present a comparative overview of clock-associated components and the circadian network in the moss P. patens.

    Results: The moss P. patens has a set of conserved circadian core components that share genetic relationship and gene expression patterns with clock genes of vascular plants. These genes include Myb-like transcription factors PpCCA1a and PpCCA1b, pseudo-response regulators PpPRR1-4, and regulatory elements PpELF3, PpLUX and possibly PpELF4. However, the moss lacks homologs of AtTOC1, AtGI and the AtZTL-family of genes, which can be found in all vascular plants studied here. These three genes constitute essential components of two of the three integrated feed-back loops in the current model of the Arabidopsis circadian clock mechanism. Consequently, our results suggest instead a single loop circadian clock in the moss. Possibly as a result of this, temperature compensation of core clock gene expression appears to be decreased in P. patens.

    Conclusions: This study is the first comparative overview of the circadian clock mechanism in a basal land plant, the moss P. patens. Our results indicate that the moss clock mechanism may represent an ancestral state in contrast to the more complex and partly duplicated structure of subsequent land plants. These findings may provide insights into the understanding of the evolution of circadian network topology.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-119235 (URN)10.1186/1471-2229-10-109 (DOI)000279959600001 ()
    Available from: 2010-02-24 Created: 2010-02-24 Last updated: 2017-12-12Bibliographically approved
  • 43.
    Holm, Karl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Gould, P.D.
    Hall, A.
    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.
    Natural variation in circadian rhythm in a worldwide sample of Capsella bursa-pastoris (Brassicaceae)Manuscript (preprint) (Other academic)
  • 44.
    Holm, Karl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Gyllenstrand, Niclas
    Department of Plant Biology and Forest Genetics, Swedish Agricultural University.
    Hedman, Harald
    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.
    Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop?2010In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 10, p. 109-Article in journal (Refereed)
    Abstract [en]

    Background: The endogenous circadian clock allows the organism to synchronize processes both to daily and seasonal changes. In plants, many metabolic processes such as photosynthesis, as well as photoperiodic responses, are under the control of a circadian clock. Comparative studies with the moss Physcomitrella patens provide the opportunity to study many aspects of land plant evolution. Here we present a comparative overview of clock-associated components and the circadian network in the moss P. patens.

    Results: The moss P. patens has a set of conserved circadian core components that share genetic relationship and gene expression patterns with clock genes of vascular plants. These genes include Myb-like transcription factors PpCCA1a and PpCCA1b, pseudo-response regulators PpPRR1-4, and regulatory elements PpELF3, PpLUX and possibly PpELF4. However, the moss lacks homologs of AtTOC1, AtGI and the AtZTL-family of genes, which can be found in all vascular plants studied here. These three genes constitute essential components of two of the three integrated feed-back loops in the current model of the Arabidopsis circadian clock mechanism. Consequently, our results suggest instead a single loop circadian clock in the moss. Possibly as a result of this, temperature compensation of core clock gene expression appears to be decreased in P. patens.

    Conclusions: This study is the first comparative overview of the circadian clock mechanism in a basal land plant, the moss P. patens. Our results indicate that the moss clock mechanism may represent an ancestral state in contrast to the more complex and partly duplicated structure of subsequent land plants. These findings may provide insights into the understanding of the evolution of circadian network topology.

  • 45.
    Holm, Karl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Peele, Hanneke
    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.
    Genetic basis for correlated variation in circadian rhythm and flowering time in the tetraploid weed Capsella bursa-pastoris (Brassicaceae)Manuscript (preprint) (Other academic)
  • 46. Ingouff, M
    et al.
    Farbos, I
    Lagercrantz, U
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    von Arnold, S
    PaHB1 is an evolutionary conserved HD-GL2 homeobox gene expressed in the protoderm during Norway spruce embryo development.2001In: Genesis, ISSN 1526-954X, Vol. 30, no 4, p. 220-30Article in journal (Refereed)
  • 47. Jarvinen, Pia
    et al.
    Palme, Anna
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Morales, Luis Orlando
    Lenanpää, Mika
    Kenainen, Marku
    Sopanen, Tuomas
    Lascoux, Martin
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Phylogenetics relationships of Betula species (Betulaceae) based on nuclear ADH and chloroplast MatK sequences2004In: American Journal of Botany, Vol. 91, p. 1834-1845Article in journal (Refereed)
  • 48.
    Kaj, I
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Mathematics. Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Krone, SM
    Lascoux, M
    Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Coalescent theory for seed bank models2001In: Journal of Applied Probability, ISSN 0021-9002, Vol. 38, no 2, p. 285-300Article in journal (Refereed)
    Abstract [en]

    We study the genealogical structure of samples from a population for which any given generation is made up of direct descendants from several previous generations. These occur in nature when there are seed banks or egg banks allowing an individual to leav

  • 49.
    Kaj, I
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Mathematics. Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Matematisk statistik.
    Lascoux, M
    Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Probability of identity by descent in metapopulations1999In: Genetics, Vol. 152, no 3, p. 1217-1228Article in journal (Refereed)
    Abstract [en]

    Equilibrium probabilities of identity by descent (IBD), for pairs of genes within individuals, for genes between individuals within subpopulations, and for genes between subpopulations are calculated in metapopulation models with fixed or varying colony sizes. A continuous-time analog to the Moran model was used in either case. For fixed-colony size both propagule and migrant pool models were considered. The varying population size model is based on a birth-death-immigration (BDI) process, to which migration between colonies is added. Wright's F statistics are calculated and compared to previous results. Adding between-island migration to the BDI model can have an important effect on the equilibrium probabilities of IBD and on Wright's index.

  • 50.
    Kaj, I
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. CONSERVATION BIOLOGY AND GENETICS.
    Lascoux, M
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Probability of identity by descent in metapopulations1999In: GENETICS, ISSN 0016-6731, Vol. 152, no 3, p. 1217-1228Article in journal (Refereed)
    Abstract [en]

    Equilibrium probabilities of identity by descent (IBD). for pairs of genes within individuals, for genes between individuals within subpopulations, and for genes between subpopulations are calculated in metapopulation models with fixed or varying colony s

123 1 - 50 of 134
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