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  • 301.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Rasmussen, Pamela C.
    Olsson, Urban
    Sundberg, Per
    Species delimitation based on multiple criteria: the Spotted Bush Warbler Bradypterus thoracicus complex (Aves : Megaluridae)2008In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 154, no 2, p. 291-307Article in journal (Refereed)
    Abstract [en]

    We demonstrate the importance of using multiple criteria in species delimitations, whatever the conceptual base for species delimitation. We do this by studying plumage, biometrics, egg coloration, song, mitochondrial DNA and habitat/altitudinal distribution in the Spotted Bush Warbler Bradypterus thoracicus (Blyth) complex, and by conducting playback experiments. Taxa that we suggest are best treated as separate species [B. thoracicus (Blyth), B. davidi (La Touche) and B. kashmirensis (Sushkin)] differ in most or all of these aspects, particularly in song and mitochondrial DNA, while those that we treat as subspecies (suschkini) or synonyms (przevalskii) differ slightly and only in morphology.

  • 302.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci SLU, Swedish Species Informat Ctr, Box 7007, S-75007 Uppsala, Sweden; Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Rasmussen, Pamela C.
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48864 USA;Michigan State Univ, MSU Museum, E Lansing, MI 48864 USA;Nat Hist Museum Tring, Bird Grp, Akeman St, Tring HP23 6AP, England.
    Xia, Canwei
    Beijing Normal Univ, Minist Educ, Coll Life Sci, Key Lab Biodivers & Ecol Engn, Beijing 100875, Peoples R China.
    Gelang, Magnus
    Gothenburg Nat Hist Museum, Box 7283, S-40235 Gothenburg, Sweden.
    Liu, Yang
    Sun Yat Sen Univ, Sch Life Sci, Dept Ecol, State Key Lab Biocontrol, Guangzhou 510275, Guangdong, Peoples R China.
    Chen, Guoling
    Sun Yat Sen Univ, Sch Life Sci, Dept Ecol, State Key Lab Biocontrol, Guangzhou 510275, Guangdong, Peoples R China.
    Zhao, Min
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China;Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
    Hao, Yan
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China;Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
    Zhao, Chao
    Cloud Mt Conservat, Dali 671003, Yunnan, Peoples R China.
    Zhao, Jian
    Sun Yat Sen Univ, Sch Life Sci, Dept Ecol, State Key Lab Biocontrol, Guangzhou 510275, Guangdong, Peoples R China.
    Yao, Chengte
    COA, Endem Species Res Inst, High Altitude Expt Stn, Chi Chi 55244, Taiwan.
    Eaton, James A.
    Birdtour Asia, 17 Keats Ave, Derby DE23 4EE, England.
    Hutchinson, Robert
    Birdtour Asia, 17 Keats Ave, Derby DE23 4EE, England.
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Systemat & Biodivers, Box 463, S-40530 Gothenburg, Sweden.
    Taxonomy of the White-browed Shortwing (Brachypteryx montana) complex on mainland Asia and Taiwan: an integrative approach supports recognition of three instead of one species2018In: Avian Research, ISSN 0005-2175, E-ISSN 2053-7166, Vol. 9, article id 34Article in journal (Refereed)
    Abstract [en]

    Background: The White-browed Shortwing (Brachypteryx montana) is widespread from the central Himalayas to the southeast Chinese mainland and the island of Taiwan, the Philippines and Indonesia. Multiple subspecies are recognised, and several of these have recently been suggested to be treated as separate species based on differences in morphology and songs.

    Methods: We here analyse plumage, morphometrics, songs, two mitochondrial and two nuclear markers, and geographical distributions of the two mainland Asian taxa B. m. cruralis and B. m. sinensis and the Taiwanese B. m. goodfellowi.

    Results: We conclude that these differ congruently in morphology, songs and DNA. Male B. m. goodfellowi is the most divergent in plumage (sexually monomorphic, unlike the two others; male similar to female), and B. m. cruralis and B. m. sinensis differ in male plumage maturation. The song of B. m. cruralis is strongly divergent from the others, whereas the songs of B. m. sinensis and B. m. goodfellowi are more similar to each other. Brachypteryx m. sinensis and B. m. goodfellowi are sisters, with an estimated divergence time 4.1 million years ago (mya; 95% highest posterior distribution [HPD] 2.8-5.5mya), and B. m. cruralis separated from these two 5.8mya (95% HPD 4.1-7.5mya). We also report notable range extensions of B. m. sinensis as well as sympatry between this taxon and B. m. cruralis in Sichuan Province, China. Brachypteryx m. montana from Java is found to be more closely related to Lesser Shortwing (B. leucophris) and Rusty-bellied Shortwing (B. hyperythra) than to the mainland Asian and Taiwanese taxa.

    Conclusion: Our data support a recent proposal to treat the three mainland Asian and Taiwanese taxa as three species, separate from B. montana sensu stricto: B. cruralis (central Himalayas to south central China and south Vietnam), B. sinensis (north central to southeastern part of mainland China) and B. goodfellowi (Taiwan Island).

  • 303.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.; Swedish Univ Agr Sci, Swedish Species Informat Ctr, Box 7007, S-75007 Uppsala, Sweden.
    Rasmussen, Pamela C
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48864 USA.; Michigan State Univ, MSU Museum, E Lansing, MI 48864 USA.; Nat Hist Museum Tring, Bird Grp, Akeman St, Tring HP23 6AP, England.
    Zhao, Chao
    Cloud Mt Conservat, Dali 671003, Peoples R China.
    Xu, Jingzi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dalvi, Shashank
    GKVK, Natl Ctr Biol Sci, Researchers Wildlife Conservat, F-21,Bellary Rd, Bengaluru 560065, Karnataka, India.
    Cai, Tianlong
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.; Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China.
    Guan, Yuyan
    Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China.; Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China.
    Zhang, Ruiying
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Kalyakin, Mikhail V.
    Lomonosov Moscow State Univ, Zool Museum, Bolshaya Nikitskaya Str 2, Moscow 125009, Russia.
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Systemat & Biodivers, Box 463, S-40530 Gothenburg, Sweden.
    Integrative taxonomy of the Plain-backed Thrush (Zoothera mollissima) complex (Aves, Turdidae) reveals cryptic species, including a new species2016In: Avian Research, ISSN 0005-2175, E-ISSN 2053-7166, Vol. 7, article id 1Article in journal (Refereed)
    Abstract [en]

    Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly sympatric.

    Methods: We revise the Z. mollissimaZ. dixoni complex by integrating morphological, acoustic, genetic (two mitochondrial and two nuclear markers), ecological and distributional datasets.

    Results: In earlier field observations, we noted two very different song types of “Plain-backed” Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and Sichuan, China (“Alpine Thrush”); a forest breeder in the eastern Himalayas and northwest Yunnan (at least), China (“Himalayan Forest Thrush”); and a forest breeder in central Sichuan (“Sichuan Forest Thrush”). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is probably true also for Alpine and Sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists (“Yunnan Thrush”). However, we find no consistent morphological differences from Alpine Thrush, and its breeding range is unknown. Molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative “Yunnan Thrush” as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato (s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocincla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto (s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest Thrush.

    Conclusions: The Plain-backed Thrush Z. mollissima s.l. comprises at least three species: Alpine Thrush Z. mollissima s.s., with a widespread alpine breeding distribution; Sichuan Forest Thrush Z. griseiceps, breeding in central Sichuan forests; and Himalayan Forest Thrush, breeding in the eastern Himalayas and northwest Yunnan (at least), which is described herein as a new species. “Yunnan Thrush” requires further study.

  • 304.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci SLU, Swedish Species Informat Ctr, Box 7007, SE-75007 Uppsala, Sweden;Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Rheindt, Frank E.
    Natl Univ Singapore, Dept Biol Sci, 16 Sci Dr 4, Singapore 117558, Singapore.
    Zhang, Ruiying
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Zhao, Min
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Wang, Jing
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Zhu, Xiaojia
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Gwee, Chyi Yin
    Natl Univ Singapore, Dept Biol Sci, 16 Sci Dr 4, Singapore 117558, Singapore.
    Hao, Yan
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Ohlson, Jan
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Box 50007, SE-10405 Stockholm, Sweden.
    Jia, Chenxi
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Prawiradilaga, Dewi M.
    Indonesian Inst Sci LIPI, Cibinong Sci Ctr, Res Ctr Biol, Jalan Raya Jakarta Bogor KM 46, Bogor 16911, Indonesia.
    Ericson, Per G. P.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Box 50007, SE-10405 Stockholm, Sweden.
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, SE-40530 Gothenburg, Sweden.
    Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 126, p. 141-152Article in journal (Refereed)
    Abstract [en]

    The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment, and we argue against proliferation of taxonomic names, and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.

  • 305. Alström, Per
    et al.
    Saitoh, Takema
    Williams, Dawn
    Nishiumi, Isao
    Shigeta, Yoshimitsu
    Ueda, Keisuke
    Irestedt, Martin
    Björklund, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Olsson, Urban
    The Arctic Warbler Phylloscopus borealis - three anciently separated cryptic species revealed2011In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 153, no 2, p. 395-410Article in journal (Refereed)
    Abstract [en]

    The Arctic Warbler Phylloscopus borealis breeds across the northern Palaearctic and northwestern-most Nearctic, from northern Scandinavia to Alaska, extending south to southern Japan, and winters in Southeast Asia, the Philippines and Indonesia. Several subspecies have been described based on subtle morphological characteristics, although the taxonomy varies considerably among different authors. A recent study (T. Saitoh et al. (2010) BMC Evol. Biol. 10: 35) identified three main mitochondrial DNA clades, corresponding to: (1) continental Eurasia and Alaska, (2) south Kamchatka, Sakhalin and northeast Hokkaido, and (3) most of Japan (Honshu, Shikoku, Kyushu). These three clades were estimated to have diverged during the late Pliocene to early Pleistocene (border at c. 2.6 million years ago). Differences in morphometrics have also been reported among members of the three clades (T. Saitoh et al. (2008) Ornithol. Sci. 7: 135-142). Here we analyse songs and calls from throughout the range of the Arctic Warbler, and conclude that these differ markedly and consistently among the populations representing the three mitochondrial clades. Kurile populations, for which no sequence data are available, are shown to belong to the second clade. To determine the correct application of available scientific names, mitochondrial DNA was sequenced from three name-bearing type specimens collected on migration or in the winter quarters. Based on the congruent variation in mitochondrial DNA, morphology and vocalizations, we propose that three species be recognized: Arctic Warbler Phylloscopus borealis (sensu stricto) (continental Eurasia and Alaska), Kamchatka Leaf Warbler Phylloscopus examinandus (Kamchatka (at least the southern part), Sakhalin, Hokkaido and Kurile Islands), and Japanese Leaf Warbler Phylloscopus xanthodryas (Japan except Hokkaido).

  • 306.
    Alström-Rapaport, Cecilia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Leskinen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Parnilo, Pekka
    Seasonal variation in the mode of reproduction of Ulva intestinalis in a brackish water environment2010In: Aquatic Botany, ISSN 0304-3770, E-ISSN 1879-1522, Vol. 93, no 4, p. 244-249Article in journal (Refereed)
    Abstract [en]

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

  • 307. 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.))
  • 308. Altekar, G
    et al.
    Dwarkadas, S
    Huelsenbeck, John
    Ronquist, Fredrik
    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, Systematic Zoology. systematisk zoologi.
    Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference2004In: Bioinformatics, Vol. 20, p. 407-415Article in journal (Refereed)
  • 309.
    Altgård, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Berggren, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Björklund, Viktor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lundsten, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Olafsson, Thorsteinn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Pettersson, Lovisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ett nytt multiplext PCR-protokoll för identifiering och detektion av Shigella och enteroinvasiv E. coli (EIEC) från livsmedel2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This report is the result of a project in the course Independent Projekt in Molecular Biotechnology at Uppsala University during the spring of 2014. The foremost purpose of the course is to give students the opportunity to carry through exstensive work in a project environment. This project was formed based on a comission from the biotechnology company SweTree Technologies, and the goal has been to compose a summary of the different techniques and methods that exist in the field of mass propagation of trees through the method of somatic embryogenesis.

    The project group has obtained information about the area mainly throgh reading patents, trying to find key components and bottlenecks in other companies’ somatic embryogenesis technologies. This paper is divided into different sections, containing the patents of the automation of different steps in the process. This is to make it easier for readers to find information about the area they are interested in, as well as to illustrate the main parts of the process as percieved by the project group.

    Currently, there are several automated solutions for almost every step in the process, some of which are already in use. All the information obtained shows that the cost and labour has decreased with the development of this technology. While there is still room for significant devolopment in order to produce a complete automated process, there is no doubt that this method is becoming an ever more important asset in the area of forestry. Our hope is that this report may be a useful tool for companies or laymen to geta grasp of the field of automated mass production of trees.

  • 310.
    Altman, S., Kirsebom, L.A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. MIKROBIOLOGI.
    Ribonuclease P1999In: RNA World (second edition), Cold Spring Harbor Press, NY , 1999, p. 351-Chapter in book (Other scientific)
  • 311. Altman, Sidney
    et al.
    Kirsebom, Leif A
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Mikrobiologi.
    Recent studies of ribonuclease P1993In: Faseb J, Vol. 7, p. 7-14Article, review/survey (Other (popular scientific, debate etc.))
  • 312. Altman, Sidney
    et al.
    Kirsebom, Leif A
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Mikrobiologi.
    Recent studies of RNase P: tRNA Structure, Biosynthesis and Function1995Chapter in book (Other (popular scientific, debate etc.))
  • 313. Altman, Sidney
    et al.
    Kirsebom, Leif A
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Mikrobiologi.
    Ribonuclease P: The RNA world Second edition1999Chapter in book (Other (popular scientific, debate etc.))
  • 314.
    Altuvia, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Wagner, E.G.H.
    Switching on and off with RNA.2000In: Proc. Natl. Acad. Sci. USA, Vol. 97, no 18, p. 9824-9826Article in journal (Refereed)
  • 315.
    Alvarez, Jose M.
    et al.
    Swedish Univ Agr Sci, Uppsala BioCtr, Dept Plant Biol, SE-75007 Uppsala, Sweden.;Linnean Ctr Plant Biol, SE-75007 Uppsala, Sweden..
    Sohlberg, Joel
    Swedish Univ Agr Sci, Uppsala BioCtr, Dept Plant Biol, SE-75007 Uppsala, Sweden.;Linnean Ctr Plant Biol, SE-75007 Uppsala, Sweden..
    Engström, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Zhu, Tianqing
    Swedish Univ Agr Sci, Uppsala BioCtr, Dept Plant Biol, SE-75007 Uppsala, Sweden.;Linnean Ctr Plant Biol, SE-75007 Uppsala, Sweden..
    Englund, Marie
    Linnean Ctr Plant Biol, SE-75007 Uppsala, Sweden.;Uppsala Univ, Dept Organismal Biol, Physiol Bot, SE-75007 Uppsala, Sweden..
    Moschou, Panagiotis N.
    Swedish Univ Agr Sci, Uppsala BioCtr, Dept Plant Biol, SE-75007 Uppsala, Sweden.;Linnean Ctr Plant Biol, SE-75007 Uppsala, Sweden..
    von Arnold, Sara
    Swedish Univ Agr Sci, Uppsala BioCtr, Dept Plant Biol, SE-75007 Uppsala, Sweden.;Linnean Ctr Plant Biol, SE-75007 Uppsala, Sweden..
    The WUSCHEL-RELATED HOMEOBOX 3 gene PaWOX3 regulates lateral organ formation in Norway spruce2015In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, no 4, p. 1078-1088Article in journal (Refereed)
    Abstract [en]

    In angiosperms, WUSCHEL-RELATED HOMEOBOX 3 (WOX3) genes are required for the recruitment of founder cells from the lateral domains of shoot meristems that form lateral regions of leaves. However, the regulation of the formation of lateral organs in gymnosperms remains unknown. By using somatic embryos of Norway spruce ( Picea abies) we have studied the expression and function of PaWOX3 during embryo development. The mRNA abundance of PaWOX3 was determined by quantitative real-time PCR, and the spatial expression of PaWOX3 was analysed by histochemical beta-glucuronidase (GUS) assays and in situ mRNA hybridization. To investigate the function of PaWOX3, we analysed how downregulation of PaWOX3 in RNA interference lines affected embryo development and morphology. PaWOX3 was highly expressed in mature embryos at the base of each cotyledon close to the junction between the cotyledons, and in the lateral margins of cotyledons and needles, separating them into an adaxial and an abaxial side. Downregulation of the expression of PaWOX3 caused defects in lateral margin outgrowth in cotyledons and needles, and reduced root elongation. Our data suggest that the WOX3 function in margin outgrowth in lateral organs is conserved among the seed plants, whereas its function in root elongation may be unique to gymnosperms.

  • 316.
    Alvarez-Castro, Jose M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Le Rouzic, Arnaud
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    How to perform meaningful estimates of genetic effects2008In: PLoS Genetics, ISSN 1553-7390, Vol. 4, no 5, p. e1000062-Article in journal (Refereed)
    Abstract [en]

    Although the genotype-phenotype map plays a central role both in Quantitative and Evolutionary Genetics, the formalization of a completely general and satisfactory model of genetic effects, particularly accounting for epistasis, remains a theoretical challenge. Here, we use a two-locus genetic system in simulated populations with epistasis to show the convenience of using a recently developed model, NOIA, to perform estimates of genetic effects and the decomposition of the genetic variance that are orthogonal even under deviations from the Hardy-Weinberg proportions. We develop the theory for how to use this model in interval mapping of quantitative trait loci using Halley-Knott regressions, and we analyze a real data set to illustrate the advantage of using this approach in practice. In this example, we show that departures from the Hardy-Weinberg proportions that are expected by sampling alone substantially alter the orthogonal estimates of genetic effects when other statistical models, like F-2 or G2A, are used instead of NOIA. Finally, for the first time from real data, we provide estimates of functional genetic effects as sets of effects of natural allele substitutions in a particular genotype, which enriches the debate on the interpretation of genetic effects as implemented both in functional and in statistical models. We also discuss further implementations leading to a completely general genotype-phenotype map.

  • 317. Alvarez-Lloret, Pedro
    et al.
    Lind, Monica
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Occupational and Environmental Medicine.
    Nyberg, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology.
    Örberg, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology.
    Rodríguez-Navarro, Alejandro B
    Effects of 3,3',4,4',5-pentachlorobiphenyl (PCB126) on vertebral bone mineralization and on thyroxin and vitamin D levels in Sprague-Dawley rats2009In: Toxicology Letters, ISSN 0378-4274, E-ISSN 1879-3169, Vol. 187, no 2, p. 63-68Article in journal (Refereed)
    Abstract [en]

    The aim of the present study is to use Fourier transform infrared spectrometry (FTIR), and transmission electron microscopy (TEM) techniques, to make a more detailed description of toxic effects of 3,3',4,4',5-pentachlorobiphenyl (PCB126) on bone tissue at the microstructural and at the molecular level as a result of an altered bone metabolism. We have analysed potential changes on vitamin D and thyroxin serum levels since these hormones represent endocrine endpoints that are critical for bone growth and development. For this purpose Sprague-Dawley rats were exposed (n=10) to PCB126 (i.p.) for 3 months (total dose, 384microg/kg bodyweight), while control rats (n=10) were injected with corn oil (vehicle). Results from FTIR showed that vertebrae from the exposed rats had an overall lower degree of mineralization (-8.5%; p<0.05) compared with the controls. In addition, results from peripheral quantitative computed tomography (pQCT) analyses showed significant increases in the trabecular bone mineral density (+12%; p<0.05) in the exposed group compared with the controls. The TEM analyses also showed an alteration in the crystallinity properties of vertebral bone mineral with a significant decrease in the size and crystallinity of apatite crystal forming the bone tissue in the exposed vs. non-exposed rats. Serum analysis revealed lower levels of thyroid hormones, FT4 (-42%; p<0.005), TT4 (-26%; p<0.005), and vitamin D (-21%; p<0.005) in exposed group compared to control animals. The complementary techniques (TEM and FTIR) used in this study have revealed insights into possible bone mineralization alteration due to PCB126 exposure. The lowering of both the thyroxin and vitamin D serum levels might be an underlying explanation for the observed effects on bone mineralization.

  • 318.
    Al-walai, Somar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Characterization of solutecarrier SLC38A62012Student paper other, 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Transport across the membrane of a cell is of crucial importance for cellular functions. The solute carrier family,SLC38 is a family of membrane proteins that transports various substances through the membrane and thusperforms many physiologically important functions, for example, transport of glutamine from astrocyte toneurons in the central nervous system. In this paper, we demonstrate that one of the transporters in this familynamed SLC38A6 forms several protein complexes with a variety of proteins in the membrane and in synapticvesicles, suggesting that SLC38A6 is involved in the synaptic release of neurotransmitters in synapses. Weperformed sensitive protein interaction analysis between the protein of interest and a variety of proteinsexpressed at different sites in the neuronal cell. We showed that SLC38A6 interacts with proteins in the cellmembrane as well as in the membrane of synaptic vesicles. The current theory is that SLC38A6 interact withthese proteins when the synaptic vesicles are in close proximity with the cell membrane during the release of theneurotransmitters.

  • 319.
    Amalia, Clausson
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hormonet leptin och dess funktioner2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 320.
    Amanda, Folkö
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The relationship between body size and dry weight in hoverflies (Syrphidae), and their movements along an urban linear landscape element2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 321.
    Amaya-Marquez, Marisol
    et al.
    Univ Nacl Colombia, Inst Ciencias Nat, Bogota 111321, Colombia.
    Tusso Gomez, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, 82152 Grosshaderner Str, Planegg Martinsried, Germany.
    Hernandez, Juan
    Univ Nacl Colombia, Inst Ciencias Nat, Bogota 111321, Colombia.
    Dario Jimenez, Juan
    Univ Nacl Colombia, Inst Ciencias Nat, Bogota 111321, Colombia.
    Wells, Harrington
    Tulsa Univ, Dept Biol, Tulsa, OK 74104 USA.
    Abramson, Charles, I
    Oklahoma State Univ, Dept Psychol, Stillwater, OK 74078 USA.
    Olfactory Learning in the Stingless Bee Melipona eburnea Friese (Apidae: Meliponini)2019In: Insects, ISSN 2075-4450, E-ISSN 2075-4450, Vol. 10, no 11, article id 412Article in journal (Refereed)
    Abstract [en]

    Olfactory learning and floral scents are co-adaptive traits in the plant-pollinator relationship. However, how scent relates to cognition and learning in the diverse group of Neotropical stingless bees is largely unknown. Here we evaluated the ability of Melipona eburnea to be conditioned to scent using the proboscis extension reflex (PER) protocol. Stingless bees did not show PER while harnessed but were able to be PER conditioned to scent when free-to-move in a mini-cage (fmPER). We evaluated the effect of: 1) unconditioned stimulus (US) reward, and 2) previous scent-reward associations on olfactory learning performance. When using unscented-US, PER-responses were low on day 1, but using scented-US reward the olfactory PER-response increased on day 1. On day 2 PER performance greatly increased in bees that previously had experienced the same odor and reward combination, while bees that experienced a different odor on day 2 showed poor olfactory learning. Bees showed higher olfactory PER conditioning to guava than to mango odor. The effect of the unconditioned stimulus reward was not a significant factor in the model on day 2. This indicates that olfactory learning performance can increase via either taste receptors or accumulated experience with the same odor. Our results have application in agriculture and pollination ecology.

  • 322.
    Amcoff, Mirjam
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Fishing for Females: Sensory Exploitation in the Swordtail Characin2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Mate choice plays an important role in sexual selection and speciation. The evolution of mate choice is intriguing in cases where choosy individuals gain little except for genetic material from the mate and where the trait used as a criterion for the choice is costly to its bearer. The sensory exploitation hypothesis is an interesting idea that applies to such cases because it suggests that sexual preferences may arise as side-effects of preferences that are under selection in other contexts. The role of mate choice in speciation is strong but is debated because the reasons for population divergence in mate preferences and sexual traits are sometimes hard to explain. Also in this context sensory exploitation offers a potential explanation in that a link between natural and sexual selection may result in divergence in sexual selection whenever populations differ in natural selection.

    In this thesis, I test several aspects of this hypothesis in a species of fish, the swordtail characin (Corynopoma riisei). In this species males display a flag-like ornament that grows from the operculum. Because females respond to this ornament by biting at it, it has been proposed to act as a food-mimic. By manipulating female food type and quantity, and testing the resulting female preference for the male ornament, I find support for the theory that the preference has evolved through sensory exploitation and that females indeed appear to relate the ornament to a food item. Furthermore, I show that sensory exploitation can lead to morphological divergence among natural populations in this species. Apart from the flag-ornament, other courtship signals are also investigated. The results show that the relative importance of different signals may vary depending on receiver motivation. This suggests that various aspects of both male courtship signals and the conditions during which they are being signalled should be considered to gain a full understanding of mate choice and its role in sexual selection and speciation.

    List of papers
    1. Does female feeding motivation affect the response to a food-mimicking male ornament in the swordtail characin Corynopoma riisei?
    Open this publication in new window or tab >>Does female feeding motivation affect the response to a food-mimicking male ornament in the swordtail characin Corynopoma riisei?
    2013 (English)In: Journal of Fish Biology, ISSN 0022-1112, E-ISSN 1095-8649, Vol. 83, no 2, p. 343-354Article in journal (Refereed) Published
    Abstract [en]

    Female response to various aspects of male trait morphology and the effect of female feeding motivation were investigated in the swordtail characin Corynopoma riisei, a species where males are equipped with a flag-like food-mimicking ornament that grows from the operculum. Unfed females responded more strongly to the male ornament and showed a stronger preference for larger ornaments than did fed females. Females were shown not to discriminate between artificial male ornaments of either undamaged or damaged shape.

    Keywords
    diet, mate preference, plasticity, sensory exploitation, signalling
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-206572 (URN)10.1111/jfb.12175 (DOI)000322547900007 ()
    Available from: 2013-09-02 Created: 2013-09-02 Last updated: 2017-12-06Bibliographically approved
    2. Sensory exploitation and plasticity in female mate choice in the swordtail characin
    Open this publication in new window or tab >>Sensory exploitation and plasticity in female mate choice in the swordtail characin
    2013 (English)In: Animal Behaviour, ISSN 0003-3472, E-ISSN 1095-8282, Vol. 85, no 5, p. 891-898Article in journal (Refereed) Published
    Abstract [en]

    Despite extensive research in the field of sexual selection, the evolutionary origin and maintenance of preferences for sexual ornaments are still debated. Recent studies have pointed out that plasticity in mate choice might be more common than previously thought, but little is still known about the factors that affect such plasticity. The swordtail characin, Corynopoma riisei, is a tropical fish species in which males use a food-mimicking ornament to attract females. We tested whether ecological factors, more specifically prior foraging experience, can affect female preference for male ornaments. For this, we habituated females on a diet consisting of either red-coloured food or standard-coloured green food items and then we tested whether female preferences for artificially red-coloured male ornaments matched their previous foraging experience. We found a strong effect of food treatment: females trained on red food showed a stronger response to males with red-coloured ornaments than females trained on green food. Our results show that ecological variation can generate divergence of female preferences for male ornaments and that the response in preference to environmental change can be rapid if the bias is partly learnt.

    Keywords
    Corynopoma riisei, diet, mate choice, sensory exploitation, sexual selection, swordtail characin
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-203305 (URN)10.1016/j.anbehav.2013.02.001 (DOI)000319332000004 ()
    Available from: 2013-07-08 Created: 2013-07-08 Last updated: 2017-12-06Bibliographically approved
    3. Diversification of a Food-Mimicking Male Ornament via Sensory Drive
    Open this publication in new window or tab >>Diversification of a Food-Mimicking Male Ornament via Sensory Drive
    2012 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 22, no 15, p. 1440-1443Article in journal (Refereed) Published
    Abstract [en]

    The evolutionary divergence of sexual signals is often important during the formation of new animal species, but our understanding of the origin of signal diversity is limited [1, 2]. Sensory drive, the optimization of communication signal efficiency through matching to the local environment, has been highlighted as a potential promoter of diversification and speciation [3]. The swordtail characin (Corynopoma riisei) is a tropical fish in which males display a flag-like ornament that elicits female foraging behavior during courtship. We show that the shape of the male ornament covaries with female diet across natural populations. More specifically, natural populations in which the female diet is more dominated by ants exhibit male ornaments more similar to the shape of an ant. Feeding experiments confirm that females habituated to a diet of ants prefer to bite at male ornaments from populations with a diet more dominated by ants. Our results show that the male ornament functions as a "fishing lure" that is diversifying in shape to match local variation in female search images employed during foraging. This direct link between variation in female feeding ecology and the evolutionary diversification of male sexual ornaments suggests that sensory drive may be a common engine of signal divergence.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-181121 (URN)10.1016/j.cub.2012.05.050 (DOI)000307415000026 ()
    Available from: 2012-09-19 Created: 2012-09-17 Last updated: 2017-12-07Bibliographically approved
    4. Courtship signalling with a labile bilateral signal: males show their best side
    Open this publication in new window or tab >>Courtship signalling with a labile bilateral signal: males show their best side
    2009 (English)In: Behavioral Ecology and Sociobiology, ISSN 0340-5443, E-ISSN 1432-0762, Vol. 63, no 12, p. 1717-1725Article in journal (Refereed) Published
    Abstract [en]

    Asymmetries in courtship signals can result from both developmental instability during ontogeny and from temporary or permanent damage following mating, fighting, or interactions with predators. These two types of asymmetries, which can be divided into fluctuating asymmetry (FA) and damage asymmetry (DA), have both been suggested to play an important role in mate choice as potential honest indicators of phenotypic and/or genetic quality, while at the same time, DA may affect ornament asymmetry in a random manner. Interestingly, despite the massive research effort that has been devoted to the study of asymmetry during the past decades, very little is known about how an individual's behaviour relates to asymmetry. Here, we measure and characterise asymmetry in morphological courtship signals in Corynopoma riisei, a fish where males carry elaborate paddle-like appendices on each side of the body that they display in front of females during courtship. Moreover, we investigate whether male courtship display, employing this bilateral morphological trait, reflects trait asymmetry. Finally, we assess whether males respond to phenotypic manipulations of DA with corresponding changes in courtship behaviour. We show that male display behaviour is asymmetric in a manner that reflects asymmetry of their morphological courtship trait and that male display behaviour responds to manipulations of asymmetry of these paddles. Our results thus suggest that males preferentially use their best side and, hence, that males respond adaptively to temporary changes in signal trait asymmetry.

    Keywords
    Sexual signalling, Sexual selection, Lateralization, Mate choice, Sensory bias, Indicator, Self-awareness
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-127482 (URN)10.1007/s00265-009-0785-7 (DOI)000270684200003 ()
    Available from: 2010-07-15 Created: 2010-07-13 Last updated: 2017-12-12Bibliographically approved
    5. Multiple male sexual signals and female responsiveness in the swordtail characin, Corynopoma riisei
    Open this publication in new window or tab >>Multiple male sexual signals and female responsiveness in the swordtail characin, Corynopoma riisei
    2015 (English)In: Environmental Biology of Fishes, ISSN 0378-1909, E-ISSN 1573-5133, Vol. 98, no 7, p. 1731-1740Article in journal (Refereed) Published
    Abstract [en]

    In the courtship process, multiple signals are often used between the signaller and the receiver. Here we describe female response to multiple male visual morphological and behavioural signals in the swordtail characin, Corynopoma riisei. The swordtail characin is a species in which males display several morphological ornaments as well as a rich courtship repertoire. Our results show that high courtship intensity was associated with an increased female response towards the male ornament, increased number of mating attempts and a reduction in female aggression. The morphological aspects investigated here did not seem to correlate with female response. This may indicate that, when both behaviour and morphology are considered simultaneously, courtship behaviour may have priority over morphological cues in this species.

    Keywords
    courtship, multiple signalling, visual cues, morphology, mate choice
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Animal Ecology
    Identifiers
    urn:nbn:se:uu:diva-207333 (URN)10.1007/s10641-015-0388-2 (DOI)000355620700001 ()
    Available from: 2013-09-12 Created: 2013-09-12 Last updated: 2017-12-06Bibliographically approved
  • 323.
    Amcoff, Mirjam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Courtship signalling with a labile bilateral signal: males show their best side2009In: Behavioral Ecology and Sociobiology, ISSN 0340-5443, E-ISSN 1432-0762, Vol. 63, no 12, p. 1717-1725Article in journal (Refereed)
    Abstract [en]

    Asymmetries in courtship signals can result from both developmental instability during ontogeny and from temporary or permanent damage following mating, fighting, or interactions with predators. These two types of asymmetries, which can be divided into fluctuating asymmetry (FA) and damage asymmetry (DA), have both been suggested to play an important role in mate choice as potential honest indicators of phenotypic and/or genetic quality, while at the same time, DA may affect ornament asymmetry in a random manner. Interestingly, despite the massive research effort that has been devoted to the study of asymmetry during the past decades, very little is known about how an individual's behaviour relates to asymmetry. Here, we measure and characterise asymmetry in morphological courtship signals in Corynopoma riisei, a fish where males carry elaborate paddle-like appendices on each side of the body that they display in front of females during courtship. Moreover, we investigate whether male courtship display, employing this bilateral morphological trait, reflects trait asymmetry. Finally, we assess whether males respond to phenotypic manipulations of DA with corresponding changes in courtship behaviour. We show that male display behaviour is asymmetric in a manner that reflects asymmetry of their morphological courtship trait and that male display behaviour responds to manipulations of asymmetry of these paddles. Our results thus suggest that males preferentially use their best side and, hence, that males respond adaptively to temporary changes in signal trait asymmetry.

  • 324.
    Amcoff, Mirjam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Gonzalez-Voyer, A.
    Kolm, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Evolution of egg dummies in Tanganyikan cichlid fishes: the roles of parental care and sexual selection2013In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 26, no 11, p. 2369-2382Article, review/survey (Refereed)
    Abstract [en]

    Sexual selection has been suggested to be an important driver of speciation in cichlid fishes of the Great Lakes of Africa, and the presence of male egg dummies is proposed to have played a key role. Here, we investigate how mouthbrooding and egg dummies have evolved in Tanganyikan cichlids, the lineage which seeded the other African radiations, with a special emphasis on the egg dummies. Using modern phylogenetic comparative analyses and a phylogeny including 86% of the 200 described species, we provide formal evidence demonstrating correlated evolution between mouthbrooding and egg dummies in Tanganyikan cichlids. These results concur with existing evidence, suggesting that egg dummies have evolved through sensory exploitation. We also demonstrate that there is a strong evolutionary correlation between the presence of egg dummies and both pre- and post-copulatory sexual selection. Moreover, egg dummy evolution was contingent on the intensity of pre- and post-copulatory sexual selection in Tanganyikan cichlids. In sum, our results provide evidence supporting the hypothesis of egg dummies evolving through sensory exploitation and highlight the role of sexual selection in favouring the evolution and maintenance of this trait.

  • 325.
    Amcoff, Mirjam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hallsson, Lara R.
    Winberg, Svante
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Kolm, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Male Courtship Pheromones Affect Female Behaviour in the Swordtail Characin ( Corynopoma riisei)2014In: Ethology, ISSN 0179-1613, E-ISSN 1439-0310, Vol. 120, no 5, p. 463-470Article in journal (Refereed)
    Abstract [en]

    Pheromones constitute an important cue used by both males and females during courtship. Here, we investigate the effect of male pheromones on female behaviour in the swordtail characin (Corynopoma riisei), a species of fish where males have a caudal pheromone gland which has been suggested to affect female behaviour during courtship. We subjected female C.riisei to male courtship pheromones and investigated the effect on both female behaviour and brain serotonergic activity levels compared to a control group. While no difference in serotonergic activity was found, the pheromone-treated females showed lower stress levels compared to the control group. Furthermore, pheromone-treated females increased locomotor activity over time, while a decrease in locomotor activity was observed in the control group. These results suggest that the male courtship pheromones may serve to reduce female stress and increase female activity, possibly to aid males in gaining access to females and facilitating sperm transfer.

  • 326.
    Amcoff, Mirjam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    A test of sensory exploitation in the swordtail characin (Corynopoma riisei) based on colour matchingbetween female prey and a male ornament2014In: Environmental Biology of Fishes, ISSN 0378-1909, E-ISSN 1573-5133, Vol. 97, no 3, p. 247-254Article in journal (Refereed)
    Abstract [en]

    The sensory exploitation hypothesis states that pre-existing biases in female sensory systems may generate strong selection on male signals to match such biases. As environmental conditions differ between populations, sexual preferences resulting from natural selection are expected to vary as well. The swordtail characin (Corynopoma riisei) is a species in which males carry a flag-like ornament growing from the operculum that has been proposed to function as a prey mimic to attract females. Here, we investigated if female plasticity in feeding preferences is associated with plasticity in preference for an artificial male ornament in this species. Females were trained for 10 days by offering them differently coloured food items and were then tested for changes in preferences for differently coloured artificial male ornaments according to foraging experience. We found a rapid and pronounced change in female preference for the colouration of the artificial ornament according to food training. Thus our results support the possibility that sensory exploitation may act as a driving force for female preferences for male ornaments in this species.

  • 327.
    Amcoff, Mirjam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Does female feeding motivation affect the response to a food-mimicking male ornament in the swordtail characin Corynopoma riisei?2013In: Journal of Fish Biology, ISSN 0022-1112, E-ISSN 1095-8649, Vol. 83, no 2, p. 343-354Article in journal (Refereed)
    Abstract [en]

    Female response to various aspects of male trait morphology and the effect of female feeding motivation were investigated in the swordtail characin Corynopoma riisei, a species where males are equipped with a flag-like food-mimicking ornament that grows from the operculum. Unfed females responded more strongly to the male ornament and showed a stronger preference for larger ornaments than did fed females. Females were shown not to discriminate between artificial male ornaments of either undamaged or damaged shape.

  • 328.
    Amcoff, Mirjam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Multiple male sexual signals and female responsiveness in the swordtail characin, Corynopoma riisei2015In: Environmental Biology of Fishes, ISSN 0378-1909, E-ISSN 1573-5133, Vol. 98, no 7, p. 1731-1740Article in journal (Refereed)
    Abstract [en]

    In the courtship process, multiple signals are often used between the signaller and the receiver. Here we describe female response to multiple male visual morphological and behavioural signals in the swordtail characin, Corynopoma riisei. The swordtail characin is a species in which males display several morphological ornaments as well as a rich courtship repertoire. Our results show that high courtship intensity was associated with an increased female response towards the male ornament, increased number of mating attempts and a reduction in female aggression. The morphological aspects investigated here did not seem to correlate with female response. This may indicate that, when both behaviour and morphology are considered simultaneously, courtship behaviour may have priority over morphological cues in this species.

  • 329.
    Amcoff, Mirjam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lindqvist, Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sensory exploitation and plasticity in female mate choice in the swordtail characin2013In: Animal Behaviour, ISSN 0003-3472, E-ISSN 1095-8282, Vol. 85, no 5, p. 891-898Article in journal (Refereed)
    Abstract [en]

    Despite extensive research in the field of sexual selection, the evolutionary origin and maintenance of preferences for sexual ornaments are still debated. Recent studies have pointed out that plasticity in mate choice might be more common than previously thought, but little is still known about the factors that affect such plasticity. The swordtail characin, Corynopoma riisei, is a tropical fish species in which males use a food-mimicking ornament to attract females. We tested whether ecological factors, more specifically prior foraging experience, can affect female preference for male ornaments. For this, we habituated females on a diet consisting of either red-coloured food or standard-coloured green food items and then we tested whether female preferences for artificially red-coloured male ornaments matched their previous foraging experience. We found a strong effect of food treatment: females trained on red food showed a stronger response to males with red-coloured ornaments than females trained on green food. Our results show that ecological variation can generate divergence of female preferences for male ornaments and that the response in preference to environmental change can be rapid if the bias is partly learnt.

  • 330.
    Amcoff, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Ecology and Evolution, Limnology.
    Elofsson, U O E
    Börjesson, H
    Norrgren, L
    Nilsson, G
    Alterations of dopaminergic and serotonergic activity in the brain of sea-run Baltic salmon suffering a thiamine deficiency-related disorder.2002In: J. Fish Biol, Vol. 60, p. 1407-1416Article in journal (Refereed)
  • 331. Amelina, Hanna
    et al.
    Apraiz, Itxaso
    Sun, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Cristobal, Susana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Proteomics-based method for the assessment of marine pollution using liquid chromatography coupled with two-dimensional electrophoresis2007In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 6, no 6, p. 2094-2104Article in journal (Refereed)
    Abstract [en]

    Using a proteomic approach, we have developed a new method for the assessment of marine pollution that generates highly reproducible protein expression patterns and it is simple and scalable. The protocol is based on applying liquid chromatography ( LC) coupled with two-dimensional electrophoresis (2DE) to analyze changes in the protein expression pattern after exposure to marine pollution. The digestive gland of the sentinel "blue mussel" ( Mytilus edulis) was batch-processed through a simple cell fractionation followed by ion-exchange chromatography and 2-DE. The selection of ligands, elution method, and small volume design was carefully considered to define a protocol that could be mainly robotized. A pilot study with samples collected from different Gothenburg harbor areas indicated that the clean area could be distinguished from the polluted ones based on a protein expression pattern ( PES) composed of 13 proteins. Principal component analysis ( PCA) and hierarchical clustering confirmed that the PES was sufficient to discriminate polluted and unpolluted areas and to provide a spatial gradient from the polluted source. Several proteins from the PES were identified by electrospray ionization tandem mass spectrometry ( ESI-MS/MS), and they are involved in,beta-oxidation, amino acid metabolism, detoxification, protein degradation, organelle biogenesis, and protein folding. In the near future, this methodology could show potential advantages to assess marine pollution and could become a stable platform to elucidate ecotoxicological questions.

  • 332.
    Ament Velásquez, Sandra Lorena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Genomic insights into the reproductive biology of Icmadophilaceae species (lichenized ascomycetes)2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Sexual reproduction or its absence has significant consequences for the evolutionary potential of a species, but little is known of the molecular basis of mating systems in non-model organisms. In Fungi, an extremely diverse and ecologically important group of Eukaryotes, sexual identity is regulated by mating type (MAT) genes with specific protein domains. The MAT genes determine if a species is capable of selfing (homothallism) or not (heterothallism). Among Fungi, almost one fifth of the species establish symbiotic associations with algae or cyanobacteria, that is, they form lichens. Yet, very few studies have explored the reproductive genetics of lichenized species. In this work, I extended current research to a poorly known family of lichen-forming fungi: the Icmadophilaceae. I used Next Generation Sequencing (NGS) genomic and transcriptomic data to produce gene models of the MAT genes and its flanking regions of four representative species. I found that the putative asexual Thamnolia vermicularis and Siphula ceratites, as well as the sexual Dibaeis baeomyces have a gene configuration concordant with heterothallism, while the sexual Icmadophila ericetorum is most likely homothallic. Additionally, I applied a number of methods to detect recombination as a proxy for cryptic sex in T. vermiculars populations from the Northern Hemisphere. Like previous studies, I found no evidence of recombination and very little genetic variation, which is at odds with the recovered structure of the MAT locus. On the other hand, a preliminary exploration of the GC content of the metagenome (including all the genomes within the lichen thallus) of S. ceratites revealed that the symbiotic association involves Alphaproteobacteria, as has been described before for taxonomically unrelated lichens but never before for this species. Overall, my results offer a wealth of information for new and more advance research into the reproductive and evolutionary biology of Icmadophilaceae species, an unexplored portion of fungal biodiversity.

  • 333.
    Ament-Velasquez, Sandra Lorena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Figuet, E.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Ballenghien, M.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Zattara, E. E.
    Indiana Univ, Dept Biol, 107 S Indiana Ave, Bloomington, IN 47405 USA.;Smithsonian Inst, Natl Museum Nat Hist, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA..
    Norenburg, J. L.
    Smithsonian Inst, Natl Museum Nat Hist, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA..
    Fernandez-Alvarez, F. A.
    CSIC Barcelona, Inst Ciencies Mar, Barcelona 08003, Spain..
    Bierne, J.
    Univ Reims, Lab Biol Cellulaire & Mol, 9 Blvd Paix, F-51100 Reims, France..
    Bierne, N.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Galtier, N.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 14, p. 3356-3369Article in journal (Refereed)
    Abstract [en]

    Comparative population genetics in asexual vs. sexual species offers the opportunity to investigate the impact of asexuality on genome evolution. Here, we analyse coding sequence polymorphism and divergence patterns in the fascinating Lineus ribbon worms, a group of marine, carnivorous nemerteans with unusual regeneration abilities, and in which asexual reproduction by fissiparity is documented. The population genomics of the fissiparous L. pseudolacteus is characterized by an extremely high level of heterozygosity and unexpectedly elevated pi(N)/pi(S) ratio, in apparent agreement with theoretical expectations under clonal evolution. Analysis of among-species allele sharing and read-count distribution, however, reveals that L. pseudolacteus is a triploid hybrid between Atlantic populations of L. sanguineus and L. lacteus. We model and quantify the relative impact of hybridity, polyploidy and asexuality on molecular variation patterns in L. pseudolacteus and conclude that (i) the peculiarities of L. pseudolacteus population genomics result in the first place from hybridization and (ii) the accumulation of new mutations through the Meselson effect is more than compensated by processes of heterozygosity erosion, such as gene conversion or gene copy loss. This study illustrates the complexity of the evolutionary processes associated with asexuality and identifies L. pseudolacteus as a promising model to study the first steps of polyploid genome evolution in an asexual context.

  • 334.
    Ameur, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    A Bioinformatics Study of Human Transcriptional Regulation2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Regulation of transcription is a central mechanism in all living cells that now can be investigated with high-throughput technologies. Data produced from such experiments give new insights to how transcription factors (TFs) coordinate the gene transcription and thereby regulate the amounts of proteins produced. These studies are also important from a medical perspective since TF proteins are often involved in disease. To learn more about transcriptional regulation, we have developed strategies for analysis of data from microarray and massively parallel sequencing (MPS) experiments.

    Our computational results consist of methods to handle the steadily increasing amount of data from high-throughput technologies. Microarray data analysis tools have been assembled in the LCB-Data Warehouse (LCB-DWH) (paper I), and other analysis strategies have been developed for MPS data (paper V). We have also developed a de novo motif search algorithm called BCRANK (paper IV).

    The analysis has lead to interesting biological findings in human liver cells (papers II-V). The investigated TFs appeared to bind at several thousand sites in the genome, that we have identified at base pair resolution. The investigated histone modifications are mainly found downstream of transcription start sites, and correlated to transcriptional activity. These histone marks are frequently found for pairs of genes in a bidirectional conformation. Our results suggest that a TF can bind in the shared promoter of two genes and regulate both of them.

    From a medical perspective, the genes bound by the investigated TFs are candidates to be involved in metabolic disorders. Moreover, we have developed a new strategy to detect single nucleotide polymorphisms (SNPs) that disrupt the binding of a TF (paper IV). We further demonstrated that SNPs can affect transcription in the immediate vicinity. Ultimately, our method may prove helpful to find disease-causing regulatory SNPs.

    List of papers
    1. The LCB Data Warehouse
    Open this publication in new window or tab >>The LCB Data Warehouse
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    2006 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 22, no 8, p. 1024-1026Article in journal (Refereed) Published
    Abstract [en]

    The Linnaeus Centre for Bioinformatics Data Warehouse (LCB-DWH) is a web-based infrastructure for reliable and secure microarray gene expression data management and analysis that provides an online service for the scientific community. The LCB-DWH is an effort towards a complete system for storage (using the BASE system), analysis and publication of microarray data. Important features of the system include: access to established methods within R/Bioconductor for data analysis, built-in connection to the Gene Ontology database and a scripting facility for automatic recording and re-play of all the steps of the analysis. The service is up and running on a high performance server. At present there are more than 150 registered users.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-97704 (URN)10.1093/bioinformatics/btl036 (DOI)16455749 (PubMedID)
    Available from: 2008-11-06 Created: 2008-11-06 Last updated: 2017-12-14Bibliographically approved
    2. Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays
    Open this publication in new window or tab >>Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays
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    2005 (English)In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 14, no 22, p. 3435-3447Article in journal (Refereed) Published
    Abstract [en]

    We present a detailed in vivo characterization of hepatocyte transcriptional regulation in HepG2 cells, using chromatin immunoprecipitation and detection on PCR fragment-based genomic tiling path arrays covering the encyclopedia of DNA element (ENCODE) regions. Our data suggest that HNF-4α and HNF-3β, which were commonly bound to distal regulatory elements, may cooperate in the regulation of a large fraction of the liver transcriptome and that both HNF-4α and USF1 may promote H3 acetylation to many of their targets. Importantly, bioinformatic analysis of the sequences bound by each transcription factor (TF) shows an over-representation of motifs highly similar to the in vitro established consensus sequences. On the basis of these data, we have inferred tentative binding sites at base pair resolution. Some of these sites have been previously found by in vitro analysis and some were verified in vitro in this study. Our data suggests that a similar approach could be used for the in vivo characterization of all predicted/uncharacterized TF and that the analysis could be scaled to the whole genome.

    Keywords
    Base Pairing/*genetics, Binding Sites/genetics, Cell Line; Tumor, Chromatin/*metabolism, Chromatin Immunoprecipitation/methods, Consensus Sequence, Genome; Human, Hepatocyte Nuclear Factor 3-beta/physiology, Hepatocyte Nuclear Factor 4/physiology, Hepatocytes/metabolism, Histones/metabolism, Humans, Metabolic Diseases/*metabolism, Oligonucleotide Array Sequence Analysis/methods, Promoter Regions (Genetics), Research Support; N.I.H.; Extramural, Research Support; Non-U.S. Gov't, Sequence Analysis; DNA, Transcription Factors/genetics/*metabolism, Upstream Stimulatory Factors/metabolism
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-80603 (URN)10.1093/hmg/ddi378 (DOI)16221759 (PubMedID)
    Available from: 2006-05-19 Created: 2006-05-19 Last updated: 2017-12-14Bibliographically approved
    3. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
    Open this publication in new window or tab >>Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
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    2008 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 18, no 3, p. 380-392Article in journal (Refereed) Published
    Abstract [en]

    Transcription factors and histone modifications are crucial regulators of gene expression that mutually influence each other. We present the DNA binding profiles of upstream stimulatory factors 1 and 2 (USF1, USF2) and acetylated histone H3 (H3ac) in a liver cell line for the whole human genome using ChIP-chip at a resolution of 35 base pairs. We determined that these three proteins bind mostly in proximity of protein coding genes transcription start sites (TSSs), and their bindings are positively correlated with gene expression levels. Based on the spatial and functional relationship between USFs and H3ac at protein coding gene promoters, we found similar promoter architecture for known genes and the novel and less-characterized transcripts human mRNAs and spliced ESTs. Furthermore, our analysis revealed a previously underestimated abundance of genes in a bidirectional conformation, where USFs are bound in between TSSs. After taking into account this promoter conformation, the results indicate that H3ac is mainly located downstream of TSS, and it is at this genomic location where it positively correlates with gene expression. Finally, USF1, which is associated to familial combined hyperlipidemia, was found to bind and potentially regulate nuclear mitochondrial genes as well as genes for lipid and cholesterol metabolism, frequently in collaboration with GA binding protein transcription factor alpha (GABPA, nuclear respiratory factor 2 [NRF-2]). This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders.

    National Category
    Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-97706 (URN)10.1101/gr.6880908 (DOI)000253766700004 ()18230803 (PubMedID)
    Available from: 2008-11-06 Created: 2008-11-06 Last updated: 2017-12-14Bibliographically approved
    4. New algorithm and ChIP-analysis identifies candidate functional SNPs
    Open this publication in new window or tab >>New algorithm and ChIP-analysis identifies candidate functional SNPs
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    In: PNASArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-97707 (URN)
    Available from: 2008-11-06 Created: 2008-11-06Bibliographically approved