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  • 251. Temperley, N.D.
    et al.
    Berlin, S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Paton, I.R.
    Griffin, D.K.
    Burt, D.W.
    Evolution of the chicken Toll-like receptor gene family: A story of gene gain and gene loss2008In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 9, p. 62-Article in journal (Refereed)
    Abstract [en]

    Background: Toll-like receptors (TLRs) perform a vital role in disease resistance through their recognition of pathogen associated molecular patterns (PAMPs). Recent advances in genomics allow comparison of TLR genes within and between many species. This study takes advantage of the recently sequenced chicken genome to determine the complete chicken TLR repertoire and place it in context of vertebrate genomic evolution. Results: The chicken TLR repertoire consists of ten genes. Phylogenetic analyses show that six of these genes have orthologs in mammals and fish, while one is only shared by fish and three appear to be unique to birds. Furthermore the phylogeny shows that TLR1-like genes arose independently in fish, birds and mammals from an ancestral gene also shared by TLR6 and TLR10. All other TLRs were already present prior to the divergence of major vertebrate lineages 550 Mya (million years ago) and have since been lost in certain lineages. Phylogenetic analysis shows the absence of TLRs 8 and 9 in chicken to be the result of gene loss. The notable exception to the tendency of gene loss in TLR evolution is found in chicken TLRs 1 and 2, each of which underwent gene duplication about 147 and 65 Mya, respectively. Conclusion: Comparative phylogenetic analysis of vertebrate TLR genes provides insight into their patterns and processes of gene evolution, with examples of both gene gain and gene loss. In addition, these comparisons clarify the nomenclature of TLR genes in vertebrates.

  • 252.
    Thulin, C-G
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Stone, J
    Tegelström, H
    Walker, CW
    Species Assignment and bygrid indentification among Scandinavian hares Öepus europaeus and L. timidus.2006In: Wildlife Biology, no 12, p. 29-38Article in journal (Refereed)
  • 253. Tngay, R.E.
    et al.
    Dawson, D.A.
    Pandhal, J.
    Clarke, Michèle L.
    David, Victor A.
    Hailer, Frank
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Culver, M.
    Isolation of 22 new Haliaeetus microsatellite loci and their characterization in the critically endangered Madagascar fish-eagle (Haliaeetus vociferoides) and three other Haliaeetus eagle species2007In: Molecular Ecology Notes, ISSN 1471-8278, E-ISSN 1471-8286, Vol. 7, no 4, p. 711-715Article in journal (Refereed)
    Abstract [en]

    We isolated a total of 22 microsatellite loci from two Haliaeetus species: the Madagascar fish-eagle (Haliaeetus vociferoides) and the bald eagle (Haliaeetus leucocephalus). Five loci were monomorphic in both the Madagascar fish-eagle (n = 24-43) and the bald eagle (n = 2-8) but were found to be polymorphic in other Haliaeetus species. Haliaeetus loci have proved useful for investigating gene flow in Haliaeetus and Aquila eagles. Ten loci were polymorphic in the critically endangered Madagascar fish-eagle and will be used to investigate the genetic population structure and mating system in this species.

  • 254. Valdiosera, C.
    et al.
    Garía-Garitagoitia, L.
    Garcia, N.
    Doadrio, I.
    Thomas, M.
    Hänni, C.
    Arsuaga, J.L.
    Barnes, I.
    Hofreiter, M.
    Orlando, L.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos)2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 13, p. 5123-5128Article in journal (Refereed)
    Abstract [en]

    The endangered brown bear populations (Ursus arctos) in Iberia have been suggested to be the last fragments of the brown bear population that served as recolonization stock for large parts of Europe during the Pleistocene. Conservation efforts are intense, and results are closely monitored. However, the efforts are based on the assumption that the Iberian bears are a unique unit that has evolved locally for an extended period. We have sequenced mitochondrial DNA (mtDNA) from ancient Iberian bear remains and analyzed them as a serial clataset, monitoring changes in diversity and occurrence of European haplogroups over time. Using these data, we show that the Iberian bear population has experienced a dynamic, recent evolutionary history. Not only has the population undergone mitochondrial gene flow from other European brown bears, but the effective population size also has fluctuated substantially. We conclude that the Iberian bear population has been a fluid evolutionary unit, developed by gene flow from other populations and population bottlenecks, far from being in genetic equilibrium or isolated from other brown bear populations. Thus, the current situation is highly unusual and the population may in fact be isolated for the first time in its history.

  • 255. Valdiosera, Cristina E.
    et al.
    García, Nuria
    Anderung, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Dalén, Love
    Crégut-Bonnoure, Evelyne
    Kahlke, Ralf-Dietrich
    Stiller, Mathias
    Brandström, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Thomas, Mark G
    Arsuaga, Juan Luis
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Barnes, Ian
    Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears.2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 24, p. 5140-5148Article in journal (Refereed)
    Abstract [en]

    Models for the development of species distribution in Europe typically invoke restriction in three temperate Mediterranean refugia during glaciations, from where recolonization of central and northern Europe occurred. The brown bear, Ursus arctos, is one of the taxa from which this model is derived. Sequence data generated from brown bear fossils show a complex phylogeographical history for western European populations. Long-term isolation in separate refugia is not required to explain our data when considering the palaeontological distribution of brown bears. We propose continuous gene flow across southern Europe, from which brown bear populations expanded after the last glaciation.

  • 256. Valdiosera, Cristina
    et al.
    Garcia, Nuria
    Dalén, Love
    Smith, Colin
    Kahlke, Ralf-Dietrich
    Lidén, Kerstin
    Angerbjörn, Anders
    Arsuaga, Juan Luis
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Typing single polymorphic nucleotides in mitochondrial DNA as a way to access Middle Pleistocene DNA2006In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 4, p. 601-603Article in journal (Refereed)
    Abstract [en]

    In this study, we have used a technique designed to target short fragments containing informative mitochondrial substitutions to extend the temporal limits of DNA recovery and study the molecular phylogeny of Ursus deningeri. We present a cladistic analysis using DNA recovered from 400 kyr old U. deningeri remains, which demonstrates U. deningeri's relation to Ursus spelaeus. This study extends the limits of recovery from skeletal remains by almost 300 kyr. Plant material from permafrost environments has yielded DNA of this age in earlier studies, and our data suggest that DNA in teeth from cave environments may be equally well preserved.

  • 257.
    Van Nieuwerburgh, Lies
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Experimental Studies on the Regulation of Pigment Dynamics in Phytoplankton and Copepods by Dissolved Inorganic Nutrients2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis examines the role of dissolved inorganic nutrients in generating changes in phytoplankton community and pigment composition and if such changes can affect the production of the antioxidant astaxanthin in the ecosystem via pelagic copepods. The background of my studies is the possible relationship between eutrophication and a reproductive disturbance in Baltic populations of Atlantic salmon (M74), which is associated with astaxanthin and thiamine deficiencies and oxidative stress. In the southern Baltic Sea, changes in nutrient loads correlate with observed trends of flagellates replacing diatoms in the phytoplankton. Copepods are the main producers of astaxanthin and a major link between phytoplankton and higher trophic levels. In laboratory and field experiments in the Baltic Sea proper and the Norwegian Sea, I show that astaxanthin synthesis in copepods is fast and depends on pigment composition of the phytoplankton diet. Among single-species diets, a diatom and a green algal cyst yielded the highest astaxanthin levels in copepods, and another diatom species, a green alga and a cyanobacterium the lowest. In nutrient-generated phytoplankton blooms in mesocosms, copepods grazing on diverse communities dominated by weakly silicified diatoms produced more astaxanthin compared with copepods grazing on communities dominated by strongly silicified diatoms. This suggests that diatoms invested in defence mechanisms and escaped grazing at surplus Si. A nutrient-starved diatom culture subjected to intraspecific competition exhibited decreased pigment levels, increased thiamine levels and increased oxidative stress.

    My results suggest that diatoms are beneficial for astaxanthin and thiamine production compared to other phytoplankton groups, but not under all circumstances. Copepod growth and development also responded to inorganic nutrient availability and affected total astaxanthin production per volume seawater, with highest production when the copepods grazed on diatoms. From an ecosystem perspective, increased N and P loads seem to promote high astaxanthin production, but not when diatoms disappear completely.

    List of papers
    1. Density-dependent patters of thiamine and pigment production in the diatom Nitzschia microcephala
    Open this publication in new window or tab >>Density-dependent patters of thiamine and pigment production in the diatom Nitzschia microcephala
    Show others...
    2003 In: Phytochemistry, Vol. 63, no 2, p. 155-163Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91657 (URN)
    Available from: 2004-04-26 Created: 2004-04-26Bibliographically approved
    2. Astaxanthin levels in copepods depend on microalgal diet
    Open this publication in new window or tab >>Astaxanthin levels in copepods depend on microalgal diet
    Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-91658 (URN)
    Available from: 2004-04-26 Created: 2004-04-26Bibliographically approved
    3. Pigment transfer from phytoplankton to zooplankton with emphasis on astaxanthin production in the Baltic Sea food web
    Open this publication in new window or tab >>Pigment transfer from phytoplankton to zooplankton with emphasis on astaxanthin production in the Baltic Sea food web
    2003 In: Marine Ecology Progress Series, Vol. 254, p. 312-224Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91659 (URN)
    Available from: 2004-04-26 Created: 2004-04-26Bibliographically approved
    4. Growth and C:N:P ratios in copepods grazing on N- or Si-limited phytoplankton blooms
    Open this publication in new window or tab >>Growth and C:N:P ratios in copepods grazing on N- or Si-limited phytoplankton blooms
    2004 (English)In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 514, no 1-3, p. 57-72Article in journal (Refereed) Published
    Abstract [en]

    The aim of this study was to investigate how nutrient limitation in phytoplankton blooms affects growth and C:N:Pratios in marine pelagic copepods.We performed two mesocosm experiments on the Atlantic coast near Trondhjem(Norway). Si-limitation in a phytoplankton bloom was triggered by N and P additions (NP treatment) and Nlimitationwas triggered by N, P and Si additions (NPSi treatment). Both nutrient treatments stimulated microalgalgrowth and increased the biomass of the phytoplankton manifold. The initial phytoplankton community consistedof flagellates and diatoms. Throughout both experiments, community composition stayed relatively stable anddiverse in the NP treatments, but in the NPSi treatments large and heavily silicified diatoms came to dominatecompletely. Phytoplankton C:N ratios in the Si-limited blooms were close to the Redfield ratio of 6.6 (on a molarbasis), but they were higher in the Control treatment without nutrient additions (ca. 8.6) and up to 14 in heavily Nlimitedblooms. When phytoplankton blooms (chlorophyll a > 25 nmol l−1) had established, wild copepods wereadded to the mesocosms. During Si-limitation the copepod density increased by ca. 40% in one of the experiments,while the C:N ratio was 5.5–6 in the copepods. During N-limitation, the copepod density stayed stable, while theC:N ratio increased to ca. 7 in the course of the experiment. In the other experiment the copepod density decreasedby ca. 25%, irrespective of nutrient treatment (C:N ratio ca. 9). The N:P ratios in the copepods varied between 16and 22 and were not different in the NP and NPSi treatments. Our study shows that N-limitation in phytoplanktoncells can increase the C:N ratio of their grazers, which has a reportedly negative effect on copepod growth andreproduction. Our study also shows that copepod populations can be regulated by seawater Si:N ratios via diatoms:at high ratios the growth from eggs/nauplii to copepodites was hampered. High Si:N ratios provide diatoms withpossibilities to escape from grazing (large species, heavy silicification, excretion of secondary metabolites), leadingto the accumulation of algal biomass without transfer to higher trophic levels.

    Keywords
    nutrient limitation, silicate, nitrogen, phosphorus, copepods, phytoplankton, mesocosm experiments
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-91660 (URN)10.1023/B:hydr.0000018206.02271.2b (DOI)
    Available from: 2004-04-26 Created: 2004-04-26 Last updated: 2017-12-14Bibliographically approved
    5. Astaxanthin levels in marine pelagic copepods grazing on two different phytoplankton diets
    Open this publication in new window or tab >>Astaxanthin levels in marine pelagic copepods grazing on two different phytoplankton diets
    Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-91661 (URN)
    Available from: 2004-04-26 Created: 2004-04-26Bibliographically approved
    6. Pigments dynamics in phytoplankton and copepods can be manipulated by inorganic nutrients
    Open this publication in new window or tab >>Pigments dynamics in phytoplankton and copepods can be manipulated by inorganic nutrients
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91662 (URN)
    Available from: 2004-04-26 Created: 2004-04-26 Last updated: 2010-01-13Bibliographically approved
  • 258.
    Van Nieuwerburgh, Lies
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wänstrand, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Liu, Jianguo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Snoeijs, Pauli
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Astaxanthin production in marine pelagic copepods grazing on two different phytoplankton diets2005In: Journal of Sea Research, ISSN 1385-1101, E-ISSN 1873-1414, Vol. 53, no 3, p. 147-160Article in journal (Refereed)
    Abstract [en]

    The red carotenoid astaxanthin is a powerful natural antioxidant of great importance in aquatic food webs where it is abundant in eggs and body tissues of fish and crustaceans. Little is known about the impact of the phytoplankton diet on astaxanthin production in copepods, its major pelagic producers. We followed the transfer of carotenoids from phytoplankton to copepods in a mesocosm experiment on the northern Atlantic coast (Norway) and recorded the astaxanthin production in copepods. Wild copepods grazed on nutrient-manipulated phytoplankton blooms, which differed in community composition and nutrient status (nitrogen or silicate limitation). The copepod pigments consisted mainly of free astaxanthin and mono- and diesters of astaxanthin. We found no significant difference in astaxanthin production per copepod individual or per unit C depending on the phytoplankton community. However, in the mesocosms astaxanthin per unit C decreased compared with natural levels, probably through a lower demand for photoprotection by the copepods in the dense phytoplankton blooms. The total astaxanthin production per litre was higher in the silicate-limited mesocosms through increased copepod density. Pigment ratio comparisons suggested that the copepod diet here consisted more of diatoms than in the nitrogen-limited mesocosms. Silicate-saturated diatoms were less grazed, possibly because they could invest more in defence mechanisms against their predators. Our study suggests that the production of astaxanthin in aquatic systems can be affected by changes in nutrient dynamics mediated by phytoplankton community composition and copepod population growth. This bottom-up force may have implications for antioxidant protection at higher trophic levels in the food web.

  • 259. Van Nieuwerburgh, Lies
    et al.
    Wänstrand, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Snoeijs, Pauli
    Growth and C:N:P ratios in copepods grazing on N- or Si-limited phytoplankton blooms2004In: Hydrobiologia, Vol. 514, p. 57-72Article in journal (Refereed)
  • 260.
    Van Nieuwerburgh, Lies
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Wänstrand, Ingrid
    Snoeijs, Pauli
    Growth and C:N:P ratios in copepods grazing on N- or Si-limited phytoplankton blooms2004In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 514, no 1-3, p. 57-72Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to investigate how nutrient limitation in phytoplankton blooms affects growth and C:N:Pratios in marine pelagic copepods.We performed two mesocosm experiments on the Atlantic coast near Trondhjem(Norway). Si-limitation in a phytoplankton bloom was triggered by N and P additions (NP treatment) and Nlimitationwas triggered by N, P and Si additions (NPSi treatment). Both nutrient treatments stimulated microalgalgrowth and increased the biomass of the phytoplankton manifold. The initial phytoplankton community consistedof flagellates and diatoms. Throughout both experiments, community composition stayed relatively stable anddiverse in the NP treatments, but in the NPSi treatments large and heavily silicified diatoms came to dominatecompletely. Phytoplankton C:N ratios in the Si-limited blooms were close to the Redfield ratio of 6.6 (on a molarbasis), but they were higher in the Control treatment without nutrient additions (ca. 8.6) and up to 14 in heavily Nlimitedblooms. When phytoplankton blooms (chlorophyll a > 25 nmol l−1) had established, wild copepods wereadded to the mesocosms. During Si-limitation the copepod density increased by ca. 40% in one of the experiments,while the C:N ratio was 5.5–6 in the copepods. During N-limitation, the copepod density stayed stable, while theC:N ratio increased to ca. 7 in the course of the experiment. In the other experiment the copepod density decreasedby ca. 25%, irrespective of nutrient treatment (C:N ratio ca. 9). The N:P ratios in the copepods varied between 16and 22 and were not different in the NP and NPSi treatments. Our study shows that N-limitation in phytoplanktoncells can increase the C:N ratio of their grazers, which has a reportedly negative effect on copepod growth andreproduction. Our study also shows that copepod populations can be regulated by seawater Si:N ratios via diatoms:at high ratios the growth from eggs/nauplii to copepodites was hampered. High Si:N ratios provide diatoms withpossibilities to escape from grazing (large species, heavy silicification, excretion of secondary metabolites), leadingto the accumulation of algal biomass without transfer to higher trophic levels.

  • 261. Vasiliauskas, Rimvydas
    et al.
    Menkis, Audrius
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Finlay, Roger D.
    Stenlid, Jan
    Wood-decay fungi in fine living roots of conifer seedlings2007In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 174, no 2, p. 441-446Article in journal (Refereed)
    Abstract [en]

    The mycorrhizal basidiomycetes are known to have multiple, independent evolutionary origins from saprotrophic ancestors. To date, a number of studies have revealed functional resemblance of mycorrhizal fungi to free-living saprotrophs, but information on the ability of saprotrophic fungi to perform as mycorrhizal symbionts is scarce. Here, the objective was to investigate the ability of three wood-decay fungi, Phlebiopsis gigantea, Phlebia centrifuga and Hypholoma fasciculare, to colonize fine roots of conifer seedlings. For each fungus, mycorrhizal syntheses were attempted with Picea abies and Pinus sylvestris. After 24 wk, isolation of fungi and direct sequencing of fungal internal transcribed spacer (ITS) rDNA were carried out from healthy-looking surface-sterilized root tips that yielded both pure cultures and ITS sequences of each inoculated strain. Mycelial mantle of P. gigantea was frequently formed on root tips of P. abies, and microscopical examination has shown the presence of intercellular hyphae inside the roots. The results provide evidence of the ability of certain wood-decay fungi to colonise fine roots of tree seedlings.

  • 262. Veeramah, Krishna R.
    et al.
    Connell, Bruce A.
    Pour, Naser Ansari
    Powell, Adam
    Plaster, Christopher A.
    Zeitlyn, David
    Mendell, Nancy R.
    Weale, Michael E.
    Bradman, Neil
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria2010In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 10, p. 92-Article in journal (Refereed)
    Abstract [en]

    Background: The Cross River region in Nigeria is an extremely diverse area linguistically with over 60 distinct languages still spoken today. It is also a region of great historical importance, being a) adjacent to the likely homeland from which Bantu-speaking people migrated across most of sub-Saharan Africa 3000-5000 years ago and b) the location of Calabar, one of the largest centres during the Atlantic slave trade. Over 1000 DNA samples from 24 clans representing speakers of the six most prominent languages in the region were collected and typed for Y-chromosome (SNPs and microsatellites) and mtDNA markers (Hypervariable Segment 1) in order to examine whether there has been substantial gene flow between groups speaking different languages in the region. In addition the Cross River region was analysed in the context of a larger geographical scale by comparison to bordering Igbo speaking groups as well as neighbouring Cameroon populations and more distant Ghanaian communities. Results: The Cross River region was shown to be extremely homogenous for both Y-chromosome and mtDNA markers with language spoken having no noticeable effect on the genetic structure of the region, consistent with estimates of inter-language gene flow of 10% per generation based on sociological data. However the groups in the region could clearly be differentiated from others in Cameroon and Ghana (and to a lesser extent Igbo populations). Significant correlations between genetic distance and both geographic and linguistic distance were observed at this larger scale. Conclusions: Previous studies have found significant correlations between genetic variation and language in Africa over large geographic distances, often across language families. However the broad sampling strategies of these datasets have limited their utility for understanding the relationship within language families. This is the first study to show that at very fine geographic/linguistic scales language differences can be maintained in the presence of substantial gene flow over an extended period of time and demonstrates the value of dense sampling strategies and having DNA of known and detailed provenance, a practice that is generally rare when investigating sub-Saharan African demographic processes using genetic data.

  • 263.
    Vila, C
    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 Biology. Evol Biol.
    Leonard, JA
    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 Biology. Evol Biol.
    Origin of dog breed diversity2006In: The Behavioural biology of dogs, CAB Internation , 2006Chapter in book (Other scientific)
  • 264.
    Vila, C
    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 Biology. Evolutionsbiologi.
    Leonard, JA
    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 Biology. Evolutionsbiologi.
    Beja-Pereira, A
    Genetic documentation of horse and donkey domestication.2006In: Documenting Domestication: New Genetic and Archaeological Paradigms., University of California Press, Berkley , 2006Chapter in book (Other scientific)
  • 265.
    Vila, C.
    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 Biology. Evolutionsbiologi.
    Leonard, J.A.
    Iriarte, A.
    O'Brien, S.J.
    Johnson, W.E.
    Wayne, R.K.
    Detecting the vanishing populations of the highly endangered Darwin's fox, Pseudalopex fulvipes.2004In: Animal Conservation, no 7, p. 147-153Article in journal (Refereed)
  • 266.
    Vilà, C.
    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 Biology. Evolutionsbiologi.
    Leonard, J.A.
    Origen de los perros del Nuevo Mundo.2004In: Investigación y Ciencia., no 329, p. 33-34Article in journal (Other (popular scientific, debate etc.))
  • 267.
    Vilà, C.
    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 Biology. Evolutionsbiologi.
    Seddon, J.
    Ellegren, 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 Biology. Evolutionsbiologi.
    Genes of domestic mammals augmented by backcrossing with wild ancestors.2005In: Trends in Genetics, no 21, p. 214-218Article in journal (Refereed)
  • 268.
    Väli, Ulo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Brandström, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Johansson, Malin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Insertion-deletion polymorphisms (indels) as genetic markers in natural populations2008In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 9, p. 8-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations. RESULTS: Sequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One hundred candidate markers (4-bp indels) were selected and genotyped in unrelated dogs (n=7) and wolves (n=18). Eighty-one and 76 out of 94 could be validated as polymorphic loci in the respective sample. Mean indel heterozygosity in a diverse set of wolves was 19%, and 74% of the loci had a minor allele frequency of >10%. Indels found to be polymorphic in wolves were subsequently genotyped in a highly bottlenecked Scandinavian wolf population. Fifty-one loci turned out to be polymorphic, showing their utility even in a population with low genetic diversity. In this population, individual heterozygosity measured at indel and microsatellite loci, respectively were highly correlated. CONCLUSIONS: With an increasing amount of sequence information gathered from non-model organisms, we suggest that indels will come to form an important source of genetic markers, easy and cheap to genotype, for studies of natural populations.

  • 269.
    Väli, Ulo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saag, Pauli
    Dombrovski, Valery
    Meyburg, Bernd-Ulrich
    Maciorowski, Grzegorz
    Mizera, Tadeusz
    Treinys, Rimgaudas
    Fagerberg, Sofie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Microsatellites and single nucleotide polymorphisms in avian hybrid identification: a comparative case study2010In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 41, no 1, p. 34-49Article in journal (Refereed)
    Abstract [en]

    The correct identification of hybrids is essential in avian hybridisation studies, but selection of the appropriate set of genetic markers for this purpose is at times complicated. Microsatellites and single nucleotide polymorphisms (SNPs) are currently the most commonly used markers in this field. We compare the efficiency of these two marker types, and their combination, in the identification of the threatened avian species, the greater spotted eagle and the lesser spotted eagle, as well as hybrids between the two species. We developed novel SNP markers from genome-wide distributed 122 candidate introns using only sympatric samples, and tested these markers successfully in 60 sympatric and allopatric spotted eagles using Bayesian model-based approaches. Comparatively, only one out of twelve previously described avian nuclear intron markers showed significant species-specific allele frequency difference, thus stressing the importance of selecting the proper markers. Twenty microsatellites outperformed selected nine SNPs in species identification, but were poorer in hybrid detection, whereas the resolution power of ten microsatellites remained too low for correct assignment. A combination of SNPs and microsatellites resulted in the most efficient and accurate identification of all individuals. Our study shows that the use of various sets of markers could lead to strikingly different assignment results, hybridisation studies may have been affected by too low a resolution power of used markers, and that an appropriate set of markers is essential for successful hybrid identification.

  • 270.
    Väli, Ülo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Einarsson, Annika
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Waits, L.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations?2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 17, p. 3808-3817Article in journal (Refereed)
    Abstract [en]

    Microsatellite variability is widely used to infer levels of genetic diversity in natural populations. However, the ascertainment bias caused by typically selecting only the most polymorphic markers in the genome may lead to reduced sensitivity for judging genome-wide levels of genetic diversity. To test this potential limitation of microsatellite-based approaches, we assessed the degree of nucleotide diversity in noncoding regions of eight different carnivore populations, including inbred as well as outbred populations, by sequencing 10 introns (5.4-5.7 kb) in 20 individuals of each population (wolves, coyotes, wolverines and lynxes). Estimates of nucleotide diversity varied 30-fold (7.1 x 10(-5)-2.1 x 10(-3)), with densities of one single nucleotide polymorphism every 112-5446 bp. Microsatellite genotyping (10-27 markers) of the same animals revealed mean multilocus heterozygosities of 0.54-0.78, a 1.4-fold difference among populations. There was a positive yet not perfect (r(2) = 0.70) correlation between microsatellite marker heterozygosity and nucleotide diversity at the population level. For example, point estimates of nucleotide diversity varied in some cases with an order of magnitude despite very similar levels of microsatellite marker heterozygosity. Moreover, at the individual level, no significant correlation was found. Our results imply that variability at microsatellite marker sets typically used in population studies may not accurately reflect the underlying genomic diversity. This suggests that researchers should consider using resequencing-based approaches for assessing genetic diversity when accurate inference is critical, as in many conservation and management contexts.

  • 271. Wayne, R.K
    et al.
    Geffen, E.
    Vilà, C.
    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 Biology. Evolutionsbiologi.
    Conservation Genetics of Canids2004In: Canids: Foxes, Wolves, Jackals and Dogs.: Status Survey and Conservation Aciton Plan, IUCN/SSC Canid Specialist Group, Gland, Switzerland. Cambridge, UK. , 2004Chapter in book (Other scientific)
  • 272. Wayne, R.K.
    et al.
    Geffen, E.
    Vilà, C.
    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 Biology. Evolutionsbiologi.
    Population and conservation genetics of canids.2004In: Biology and Conservation of Wild Canids., Oxford University Press , 2004Chapter in book (Other scientific)
  • 273.
    Webster, Matthew T
    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 Biology. Evolutionsbiologi.
    Axelsson, Erik
    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 Biology. Evolutionsbiologi.
    Ellegren, Hans
    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 Biology. Evolutionsbiologi.
    Strong regional biases in nucleotide substitution in the chicken genome.2006In: Mol Biol Evol, ISSN 0737-4038, Vol. 23, no 6, p. 1203-16Article in journal (Refereed)
    Abstract [en]

    Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. websterm@tcd.ie

    Interspersed repeats have emerged as a valuable tool for studying neutral patterns of molecular evolution. Here we analyze variation in the rate and pattern of nucleotide substitution across all autosomes in the chicken genome by comparing the present-day CR1 repeat sequences with their ancestral copies and reconstructing nucleotide substitutions with a maximum likelihood model. The results shed light on the origin and evolution of large-scale heterogeneity in GC content found in the genomes of birds and mammals--the isochore structure. In contrast to mammals, where GC content is becoming homogenized, heterogeneity in GC content is being reinforced in the chicken genome. This is also supported by patterns of substitution inferred from alignments of introns in chicken, turkey, and quail. Analysis of individual substitution frequencies is consistent with the biased gene conversion (BGC) model of isochore evolution, and it is likely that patterns of evolution in the chicken genome closely resemble those in the ancestral amniote genome, when it is inferred that isochores originated. Microchromosomes and distal regions of macrochromosomes are found to have elevated substitution rates and a more GC-biased pattern of nucleotide substitution. This can largely be accounted for by a strong correlation between GC content and the rate and pattern of substitution. The results suggest that an interaction between increased mutability at CpG motifs and fixation biases due to BGC could explain increased levels of divergence in GC-rich regions.

  • 274.
    Webster, Matthew T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hagberg, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Is there evidence for convergent evolution around human microsatellites?2007In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 5, p. 1097-1100Article in journal (Refereed)
    Abstract [en]

    A study by Vowles and Amos (2004) identified atypical patterns of base composition around human microsatellites and argued that microsatellites generate mutational biases in their flanking regions. Here, we perform simulations of molecular evolution using a simple model that suggest similar patterns can be produced without any such biases in genome evolution.

  • 275.
    Webster, Matthew T
    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 Biology. Evolutionsbiologi.
    Smith, Nick G C
    Hultin-Rosenberg, Lina
    Arndt, Peter F
    Ellegren, Hans
    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 Biology. Evolutionsbiologi.
    Male-driven biased gene conversion governs the evolution of base composition in human alu repeats.2005In: Mol Biol Evol, ISSN 0737-4038, Vol. 22, no 6, p. 1468-74Article in journal (Refereed)
    Abstract [en]

    Regional biases in substitution pattern are likely to be responsible for the large-scale variation in base composition observed in vertebrate genomes. However, the evolutionary forces responsible for these biases are still not clearly defined. In order to study the processes of mutation and fixation across the entire human genome, we analyzed patterns of substitution in Alu repeats since their insertion. We also studied patterns of human polymorphism within the repeats. There is a highly significant effect of recombination rate on the pattern of substitution, whereas no such effect is seen on the pattern of polymorphism. These results suggest that regional biases in substitution are caused by biased gene conversion, a process that increases the probability of fixation of mutations that increase GC content. Furthermore, the strongest correlate of substitution patterns is found to be male recombination rates rather than female or sex-averaged recombination rates. This indicates that in addition to sexual dimorphism in recombination rates, the sexes also differ in the relative rates of crossover and gene conversion.

  • 276.
    Webster, Matthew T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, Nick G.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Lercher, M.J.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Gene expression, synteny, and local similarity in human noncoding mutation rates2004In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 21, no 10, p. 1820-1830Article in journal (Refereed)
    Abstract [en]

    The human genome is organized with regard to many features such as isochores, Giemsa bands, clusters of genes with similar expression patterns, and contiguous regions with shared evolutionary histories (synteny blocks). In addition to these genomic features, it is clear that mutation rates also vary across the human genome. To address how mutation rates and genomic features are related, we analyzed substitution rates at three classes of putatively neutral noncoding sites (nongenic, intronic, and ancestral repeats) in approximately 14 Mb of human-chimpanzee alignments covering human chromosome 7. Patterns of mutation rate variation inferred from substitution rate variation differ among the three site classes. In particular, we find that intronic mutation rates are strongly affected by the breadth of expression of the genes in which they reside, with broadly expressed genes exhibiting low mutation rates, probably as a consequence of the transcription-coupled repair process acting in the germ line. All site classes show significant local similarities in mutation rate at the megabase scale, and regional similarities in nongenic mutation rate covary with blocks of synteny between the human and mouse genomes, indicating that the evolutionary history of a genomic region is an important determinant of mutation rate.

  • 277.
    Webster, Matthew Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, Nick G.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Fixation biases affecting human SNPs?2004In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 20, no 3, p. 122-126Article in journal (Refereed)
    Abstract [en]

    Under neutrality all classes of mutation have an equal probability of becoming fixed in a population. In this article, we describe our analysis of the frequency distributions of >5000 human SNPs and provide evident of biases in the process of fixation of certain classes of point mutation that are most likely to be attributable to biased gene conversion. The results indicate an increased fixation probability of mutations that result in the incorporation of a GC base pair. Furthermore, in transcribed regions this process exhibits strand asymmetry, and is biased towards preserving a G base on the coding strand. Biased gene conversion has the potential to explain both existence of isochores and the compositional asymmetry in mammalian transcribed regions.

  • 278. Wik, Lotta
    et al.
    Karlsson, Magnus
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behavior of taxa2008In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, no 1, p. 109-Article in journal (Refereed)
    Abstract [en]

    Background: Comparative sequencing studies among a wide range of taxonomic groups, including fungi, have led to the discovery that reproductive genes evolve more rapidly than other genes. However, for fungal reproductive genes the question has remained whether the rapid evolution is a result of stochastic or deterministic processes. The mating-type (mat) genes constitute the master regulators of sexual reproduction in filamentous ascomycetes and here we present a study of the molecular evolution of the four mat-genes (mat a-1, mat A-1, mat A-2 and mat A-3) of 20 Neurospora taxa. Results: We estimated nonsynonymous and synonymous substitution rates of genes to infer their evolutionary rate, and confirmed that the mat-genes evolve rapidly. Furthermore, the evolutionary trajectories are related to the reproductive modes of the taxa; likelihood methods revealed that positive selection acting on specific codons drives the diversity in heterothallic taxa, while among homothallic taxa the rapid evolution is due to a lack of selective constraint. The latter finding is supported by presence of stop codons and frame shift mutations disrupting the open reading frames of mat a-1, mat A-2 and mat A-3 in homothallic taxa. Lower selective constraints of matgenes was found among homothallic than heterothallic taxa, and comparisons with nonreproductive genes argue that this disparity is not a nonspecific, genome-wide phenomenon. Conclusion: Our data show that the mat-genes evolve rapidly in Neurospora. The rapid divergence is due to either adaptive evolution or lack of selective constraints, depending on the reproductive mode of the taxa. This is the first instance of positive selection acting on reproductive genes in the fungal kingdom, and illustrates how the evolutionary trajectory of reproductive genes can change after a switch in reproductive behaviour of an organism.

  • 279.
    Wolf, Jochen B. W.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Kuenstner, Axel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Nam, Kiwoong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Nonlinear Dynamics of Nonsynonymous (d(N)) and Synonymous (d(S)) Substitution Rates Affects Inference of Selection2009In: Genome Biology and Evolution, ISSN 1759-6653, Vol. 1, p. 308-319Article in journal (Refereed)
    Abstract [en]

    Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the mode and strength of selection. To control for regional variation in substitution rates, the proportionate number of nonsynonymous differences (d(N)) is divided by the proportionate number of synonymous differences (d(S)). The resulting ratio (d(N)/d(S)) is a widely used indicator for functional divergence to identify particular genes that underwent positive selection. With the ever-growing amount of genome data, summary statistics like mean d(N)/d(S) allow gathering information on the mode of evolution for entire species. Both applications hinge on the assumption that d(S) and mean d(S) (similar to branch length) are neutral and adequately control for variation in substitution rates across genes and across organisms, respectively. We here explore the validity of this assumption using empirical data based on whole-genome protein sequence alignments between human and 15 other vertebrate species and several simulation approaches. We find that d(N)/d(S) does not appropriately reflect the action of selection as it is strongly influenced by its denominator (d(S)). Particularly for closely related taxa, such as human and chimpanzee, d(N)/d(S) can be misleading and is not an unadulterated indicator of selection. Instead, we suggest that inconsistencies in the behavior of d(N)/d(S) are to be expected and highlight the idea that this behavior may be inherent to taking the ratio of two randomly distributed variables that are nonlinearly correlated. New null hypotheses will be needed to adequately handle these nonlinear dynamics.

  • 280. Wong, Gane Ka-Shu
    et al.
    Liu, Bin
    Wang, Jun
    Zhang, Yong
    Yang, Xu
    Zhang, Zengjin
    Meng, Qingshun
    Zhou, Jun
    Li, Dawei
    Zhang, Jingjing
    Ni, Peixiang
    Li, Songgang
    Ran, Longhua
    Li, Heng
    Zhang, Jianguo
    Li, Ruiqiang
    Li, Shengting
    Zheng, Hongkun
    Lin, Wei
    Li, Guangyuan
    Wang, Xiaoling
    Zhao, Wenming
    Li, Jun
    Ye, Chen
    Dai, Mingtao
    Ruan, Jue
    Zhou, Yan
    Li, Yuanzhe
    He, Ximiao
    Zhang, Yunze
    Wang, Jing
    Huang, Xiangang
    Tong, Wei
    Chen, Jie
    Ye, Jia
    Chen, Chen
    Wei, Ning
    Li, Guoqing
    Dong, Le
    Lan, Fengdi
    Sun, Yongqiao
    Zhang, Zhenpeng
    Yang, Zheng
    Yu, Yingpu
    Huang, Yanqing
    He, Dandan
    Xi, Yan
    Wei, Dong
    Qi, Qiuhui
    Li, Wenjie
    Shi, Jianping
    Wang, Miaoheng
    Xie, Fei
    Wang, Jianjun
    Zhang, Xiaowei
    Wang, Pei
    Zhao, Yiqiang
    Li, Ning
    Yang, Ning
    Dong, Wei
    Hu, Songnian
    Zeng, Changqing
    Zheng, Weimou
    Hao, Bailin
    Hillier, Ladeana W
    Yang, Shiaw-Pyng
    Warren, Wesley C
    Wilson, Richard K
    Brandström, Mikael
    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 Biology. Evolutionsbiologi.
    Ellegren, Hans
    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 Biology. Evolutionsbiologi.
    Crooijmans, Richard P M A
    van der Poel, Jan J
    Bovenhuis, Henk
    Groenen, Martien A M
    Ovcharenko, Ivan
    Gordon, Laurie
    Stubbs, Lisa
    Lucas, Susan
    Glavina, Tijana
    Aerts, Andrea
    Kaiser, Pete
    Rothwell, Lisa
    Young, John R
    Rogers, Sally
    Walker, Brian A
    van Hateren, Andy
    Kaufman, Jim
    Bumstead, Nat
    Lamont, Susan J
    Zhou, Huaijun
    Hocking, Paul M
    Morrice, David
    de Koning, Dirk-Jan
    Law, Andy
    Bartley, Neil
    Burt, David W
    Hunt, Henry
    Cheng, Hans H
    Gunnarsson, Ulrika
    Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Wahlberg, Per
    Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Andersson, Leif
    Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Kindlund, Ellen
    Tammi, Martti T
    Andersson, Björn
    Webber, Caleb
    Ponting, Chris P
    Overton, Ian M
    Boardman, Paul E
    Tang, Haizhou
    Hubbard, Simon J
    Wilson, Stuart A
    Yu, Jun
    Wang, Jian
    Yang, Huanming
    A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.2004In: Nature, ISSN 1476-4687, Vol. 432, no 7018, p. 717-22Article in journal (Refereed)
  • 281.
    Wänstrand, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Pigment and Thiamine Dynamics in Marine Phytoplankton and Copepods2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Based on a field study and several mesocosm experiments, I evaluated the use of pigments as chemotaxonomical biomarkers for phytoplankton community composition in the Baltic Sea and I examined effects of inorganic nutrients on the dynamics of carotenoids and thiamine (vitamin B1) at the phytoplankton–copepod level in marine pelagic food webs.

    My results show that HPLC pigment analysis combined with CHEMTAX data processing was an accurate alternative to microscopic analysis of Baltic Sea phytoplankton.

    Experimental supply of N, P and Si affected copepod growth and biochemical status via changes in biomass and composition of their phytoplankton diet. Net population growth rates were generally higher when phytoflagellates dominated (low Si:N ratio) and lower when diatoms dominated (high Si:N ratio).

    Copepod body concentrations of astaxanthin decreased with fertilization. Correlations with reduced under-water irradiance were consistent with the photo-protective function of this antioxidant. Thiamine concentrations in phytoplankton also decreased with fertilization. In copepods, low Si:N ratios resulted in higher thiamine concentrations than high Si:N ratios. Thiamine concentration and degree of phosphorylation were useful as indicators of thiamine shortage both in phytoplankton and copepods. The concentrations of thiamine and astaxanthin in the copepod communities were positively correlated.

    As copepods constitute a major link between pelagic primary producers and higher trophic levels, fertilization effects may be responsible for astaxanthin and thiamine deficiencies in salmon suffering from the M74 syndrome, which appeared concurrently with large-scale eutrophication in the Baltic Sea. As both thiamine and astaxanthin are deficient in M74-affected salmon, there is a need for physiological and molecular investigations of possible interactions between the two compounds in living cells.

    List of papers
    1. Seasonal phytoplankton pigment dynamics in the northern Baltic Sea: assessment by ships-of-opportunity
    Open this publication in new window or tab >>Seasonal phytoplankton pigment dynamics in the northern Baltic Sea: assessment by ships-of-opportunity
    (English)Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-92153 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2009-03-31Bibliographically approved
    2. Phytoplankton community dynamics in nutrient-enriched mesocosms in the Baltic Sea: a chemotaxonomical approach
    Open this publication in new window or tab >>Phytoplankton community dynamics in nutrient-enriched mesocosms in the Baltic Sea: a chemotaxonomical approach
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92154 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2010-01-14Bibliographically approved
    3. Growth and C:N:P ratios in copepods grazing on N- or Si-limited phytoplankton blooms
    Open this publication in new window or tab >>Growth and C:N:P ratios in copepods grazing on N- or Si-limited phytoplankton blooms
    2004 (English)In: Hydrobiologia, Vol. 514, p. 57-72Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92155 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2009-03-31Bibliographically approved
    4. Astaxanthin production in marine pelagic copepods grazing on two different phytoplankton diets
    Open this publication in new window or tab >>Astaxanthin production in marine pelagic copepods grazing on two different phytoplankton diets
    2005 (English)In: Journal of Sea Research, ISSN 1385-1101, E-ISSN 1873-1414, Vol. 53, no 3, p. 147-160Article in journal (Refereed) Published
    Abstract [en]

    The red carotenoid astaxanthin is a powerful natural antioxidant of great importance in aquatic food webs where it is abundant in eggs and body tissues of fish and crustaceans. Little is known about the impact of the phytoplankton diet on astaxanthin production in copepods, its major pelagic producers. We followed the transfer of carotenoids from phytoplankton to copepods in a mesocosm experiment on the northern Atlantic coast (Norway) and recorded the astaxanthin production in copepods. Wild copepods grazed on nutrient-manipulated phytoplankton blooms, which differed in community composition and nutrient status (nitrogen or silicate limitation). The copepod pigments consisted mainly of free astaxanthin and mono- and diesters of astaxanthin. We found no significant difference in astaxanthin production per copepod individual or per unit C depending on the phytoplankton community. However, in the mesocosms astaxanthin per unit C decreased compared with natural levels, probably through a lower demand for photoprotection by the copepods in the dense phytoplankton blooms. The total astaxanthin production per litre was higher in the silicate-limited mesocosms through increased copepod density. Pigment ratio comparisons suggested that the copepod diet here consisted more of diatoms than in the nitrogen-limited mesocosms. Silicate-saturated diatoms were less grazed, possibly because they could invest more in defence mechanisms against their predators. Our study suggests that the production of astaxanthin in aquatic systems can be affected by changes in nutrient dynamics mediated by phytoplankton community composition and copepod population growth. This bottom-up force may have implications for antioxidant protection at higher trophic levels in the food web.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-92156 (URN)10.1016/j.seares.2004.07.003 (DOI)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2017-12-14Bibliographically approved
    5. Inorganic nutrients regulate astaxanthin production in copepods via phytoplankton community dynamics
    Open this publication in new window or tab >>Inorganic nutrients regulate astaxanthin production in copepods via phytoplankton community dynamics
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    (English)Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-92157 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2009-03-31Bibliographically approved
    6. Thiamine (vitamin B1) dynamics in phytoplankton and copepods is regulated by inorganic nutrient supply
    Open this publication in new window or tab >>Thiamine (vitamin B1) dynamics in phytoplankton and copepods is regulated by inorganic nutrient supply
    Show others...
    (English)Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-92158 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2009-03-31Bibliographically approved
  • 282.
    Wänstrand, Ingrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Barros, Marcelo Paes de
    Pinto, Ernani
    Pedersén, Marianne
    Snoeijs, Pauli
    Inorganic nutrients regulate astaxanthin production in copepods via phytoplankton community dynamicsArticle in journal (Refereed)
  • 283.
    Wänstrand, Ingrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Snoeijs, Pauli
    Phytoplankton community dynamics in nutrient-enriched mesocosms in the Baltic Sea: a chemotaxonomical approachManuscript (Other (popular science, discussion, etc.))
  • 284.
    Wänstrand, Ingrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Snoeijs, Pauli
    Seasonal phytoplankton pigment dynamics in the northern Baltic Sea: assessment by ships-of-opportunityArticle in journal (Refereed)
  • 285.
    Åberg, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Finding Genes for Schizophrenia2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Schizophrenia is one of our most common psychiatric diseases. It severely affects all aspects of psychological functions and results in loss of contact with reality. No cure exists and the treatments available today produce only partial relief for disease symptoms. The aim of this work is to better understand the etiology of schizophrenia by identification of candidate genes and gene pathways involved in the development of the disease.

    In a preliminarily study, the effects of medication and genetic factors were investigated in a candidate gene, serotonin 2C receptor. This study distinguished pharmacological effects, caused by neuroleptics, and/or genetic effects, caused by unique polymorphisms, from other effects responsible for mRNA expression changes on candidate genes.

    The core of the thesis describes a new candidate gene for schizophrenia, the quaking homolog, KH domain RNA binding (mouse) or QKI, located on chromosome 6q26-q27. The identification of QKI is supported by previous linkage studies, current association studies and mRNA expression studies using three different sample sets. The investigated samples included a 12-generation pedigree with 16 distantly related schizophrenic cases and their parents, 176 unrelated nuclear families with at least one affected child in each family and human brain autopsies from 55 schizophrenic cases and from 55 controls. Indirect evidence showing involvement of QKI in myelin regulation of central nervous system is presented. Myelin plays an important role in development of normal brains and disruption of QKI might lead to schizophrenia symptoms.

    In a forth sample set, including extended pedigrees originated from a geographically isolated area above the Arctic Circle, in northeast Sweden, two additional schizophrenia susceptibility loci were identified, 2q13 and 5q21. Both these regions have previously been highlighted as potential schizophrenia loci in several other investigations, including a large Finnish study. This suggests common schizophrenia susceptibility loci for Nordic populations.

    A pilot investigation including a genome wide haplotype analysis is presented. This statistical strategy could be further developed and applied to the artic Swedish families, including analysis of 900 microsatellites and 10,000 SNPs.

    These findings will facilitate the understanding of the schizophrenia etiology and may lead to development of more efficient treatments for patients that suffer from schizophrenia.