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  • 51.
    Andersson, Jan O
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv GE
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Insights into the evolutionary process of genome degradation1999In: Current Opinion in Genetics and Development, ISSN 0959-437X, E-ISSN 1879-0380, Vol. 9, no 6, p. 664-671Article in journal (Refereed)
    Abstract [en]

    Studies of noncoding and pseudogene sequence diversity, particularly in Rickettsia, have begun to reveal the basic principles of genome degradation in microorganisms. Increasingly, studies of genes and genomes suggest that there has been an extensive amount of horizontal gene transfer among microorganisms. As this inflow of genetic material does not seem generally to have resulted in genome size expansions, however, degenerative processes must be at the very least as widespread as horizontal gene transfer. The basic principles of gene degradation and elimination that are being explored in Rickettsia are likely to be of major importance for our understanding of how microbial genomes evolve.

  • 52.
    Andersson, Jan O
    et al.
    Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada.
    Doolittle, W Ford
    Nesbø, Camilla L
    Genomics. Are there bugs in our genome?2001In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 292, no 5523, p. 1848-1850Article in journal (Refereed)
  • 53.
    Andersson, Jan O.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hirt, Robert P.
    Foster, Peter G.
    Roger, Andrew J.
    Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes2006In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 6, article id 27Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses. RESULTS: The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time. CONCLUSION: Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.

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  • 54.
    Andersson, Jan O
    et al.
    The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada.
    Roger, Andrew J
    A cyanobacterial gene in nonphotosynthetic protists: an early chloroplast acquisition in eukaryotes?2002In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 12, no 2, p. 115-119Article in journal (Refereed)
    Abstract [en]

    Since the incorporation of mitochondria and chloroplasts (plastids) into the eukaryotic cell by endosymbiosis, genes have been transferred from the organellar genomes to the nucleus of the host, via an ongoing process known as endosymbiotic gene transfer. Accordingly, in photosynthetic eukaryotes, nuclear genes with cyanobacterial affinity are believed to have originated from endosymbiotic gene transfer from chloroplasts. Analysis of the Arabidopsis thaliana genome has shown that a significant fraction (2%-9%) of the nuclear genes have such an endosymbiotic origin. Recently, it was argued that 6-phosphogluconate dehydrogenase (gnd)-the second enzyme in the oxidative pentose phosphate pathway-was one such example. Here we show that gnd genes with cyanobacterial affinity also are present in several nonphotosynthetic protistan lineages, such as Heterolobosea, Apicomplexa, and parasitic Heterokonta. Current data cannot definitively resolve whether these groups acquired the gnd gene by primary and/or secondary endosymbiosis or via an independent lateral gene transfer event. Nevertheless, our data suggest that chloroplasts were introduced into eukaryotes much earlier than previously thought and that several major groups of heterotrophic eukaryotes have secondarily lost photosynthetic plastids.

  • 55.
    Andersson, Jan O
    et al.
    The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada..
    Roger, Andrew J
    Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers2002In: Eukaryotic Cell, ISSN 1535-9778, E-ISSN 1535-9786, Vol. 1, no 2, p. 304-310Article in journal (Refereed)
    Abstract [en]

    Lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. Except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. Here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by gltD) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by sudA). The scattered distribution of the sudA and sudB gene pair and the phylogenetic analysis strongly suggest that lateral gene transfer was involved in the propagation of the genes in the three domains of life. One of these transfers most likely occurred between a prokaryote and an ancestor of diplomonad protists. Furthermore, phylogenetic analyses indicate that the gene for the small subunit of glutamate synthase was transferred from a low-GC gram-positive bacterium to a common ancestor of animals, fungi, and plants. Interestingly, in both examples, the eukaryotes encode a single gene that corresponds to a conserved operon structure in prokaryotes. Our analyses, together with several recent publications, show that lateral gene transfers from prokaryotes to unicellular eukaryotes occur with appreciable frequency. In the case of the genes for sulfide dehydrogenase, the transfer affected only a limited group of eukaryotes--the diplomonads--while the transfer of the glutamate synthase gene probably happened earlier in evolution and affected a wider range of eukaryotes.

  • 56.
    Andersson, Jan O
    et al.
    The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada.
    Sjögren, Åsa M
    Davis, Lesley A M
    Embley, T Martin
    Roger, Andrew J
    Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes2003In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 13, no 2, p. 94-104Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary mechanism among prokaryotes. The situation in eukaryotes is less clear; the human genome sequence failed to give strong support for any recent transfers from prokaryotes to vertebrates, yet a number of LGTs from prokaryotes to protists (unicellular eukaryotes) have been documented. Here, we perform a systematic analysis to investigate the impact of LGT on the evolution of diplomonads, a group of anaerobic protists.

    RESULTS: Phylogenetic analyses of 15 genes present in the genome of the Atlantic Salmon parasite Spironucleus barkhanus and/or the intestinal parasite Giardia lamblia show that most of these genes originated via LGT. Half of the genes are putatively involved in processes related to an anaerobic lifestyle, and this finding suggests that a common ancestor, which most probably was aerobic, of Spironucleus and Giardia adapted to an anaerobic environment in part by acquiring genes via LGT from prokaryotes. The sources of the transferred diplomonad genes are found among all three domains of life, including other eukaryotes. Many of the phylogenetic reconstructions show eukaryotes emerging in several distinct regions of the tree, strongly suggesting that LGT not only involved diplomonads, but also involved other eukaryotic groups.

    CONCLUSIONS: Our study shows that LGT is a significant evolutionary mechanism among diplomonads in particular and protists in general. These findings provide insights into the evolution of biochemical pathways in early eukaryote evolution and have important implications for studies of eukaryotic genome evolution and organismal relationships. Furthermore, "fusion" hypotheses for the origin of eukaryotes need to be rigorously reexamined in the light of these results.

  • 57.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Stress management strategies in single bacterial cells2016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 15, p. 3921-3923Article in journal (Other academic)
  • 58. Andersson, Siv G E
    et al.
    Alsmark, Cecilia
    Canbäck, Björn
    Davids, Wagied
    Frank, Carolin
    Karlberg, Olof
    Klasson, Lisa
    Antoine-Legault, Boris
    Mira, Alex
    Tamas, Ivica
    Comparative genomics of microbial pathogens and symbionts.2002In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 18 Suppl 2, p. S17-Article in journal (Refereed)
    Abstract [en]

    We are interested in quantifying the contribution of gene acquisition, loss, expansion and rearrangements to the evolution of microbial genomes. Here, we discuss factors influencing microbial genome divergence based on pair-wise genome comparisons of closely related strains and species with different lifestyles. A particular focus is on intracellular pathogens and symbionts of the genera Rickettsia, Bartonella and BUCHNERA: Extensive gene loss and restricted access to phage and plasmid pools may provide an explanation for why single host pathogens are normally less successful than multihost pathogens. We note that species-specific genes tend to be shorter than orthologous genes, suggesting that a fraction of these may represent fossil-orfs, as also supported by multiple sequence alignments among species. The results of our genome comparisons are placed in the context of phylogenomic analyses of alpha and gamma proteobacteria. We highlight artefacts caused by different rates and patterns of mutations, suggesting that atypical phylogenetic placements can not a priori be taken as evidence for horizontal gene transfer events. The flexibility in genome structure among free-living microbes contrasts with the extreme stability observed for the small genomes of aphid endosymbionts, in which no rearrangements or inflow of genetic material have occurred during the past 50 millions years (1). Taken together, the results suggest that genomic stability correlate with the content of repeated sequences and mobile genetic elements, and thereby indirectly with bacterial lifestyles.

  • 59.
    Andersson, Siv GE
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Zomorodipour, A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Andersson, Jan O
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Sicheritz-Ponten, T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Alsmark, UCM
    Uppsala University.
    Podowski, RM
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Näslund, A Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Eriksson, Ann-Sofie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Winkler, HH
    Kurland, Charles G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    The genome sequence of Rickettsia prowazekii and the origin of mitochondria1998In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 396, no 6707, p. 133-140Article in journal (Refereed)
    Abstract [en]

    We describe here the complete genome sequence (1,111,523 base pairs) of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria. Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria. Such genes seem to have been replaced by homologues in the nuclear (host) genome. The R. prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a microbial genome. Such non-coding sequences may be degraded remnants of 'neutralized' genes that await elimination from the genome. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.

  • 60.
    Andrade, Pedro
    et al.
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal;Univ Porto, Dept Biol, Fac Ciencias, P-4169007 Porto, Portugal.
    Pinho, Catarina
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal.
    Perez i de lanuza, Guillem
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal.
    Afonso, Sandra
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal.
    Brejcha, Jindrich
    Charles Univ Prague, Fac Sci, Dept Philosophy & Hist Sci, Prague 12800 2, Czech Republic;Natl Museum, Dept Zool, Prague 19300, Czech Republic;Univ Valencia, Cavanilles Inst Biodivers & Evolutionary Biol, Ethol Lab, Paterna 46980, Spain.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wallerman, Ola
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pereira, Paulo
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal;Univ Porto, Dept Biol, Fac Ciencias, P-4169007 Porto, Portugal.
    Sabatino, Stephen J.
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal.
    Bellati, Adriana
    Univ Pavia, Dept Earth & Environm Sci, I-27100 Pavia, Italy.
    Pellitteri-Rosa, Daniele
    Univ Pavia, Dept Earth & Environm Sci, I-27100 Pavia, Italy.
    Bosakova, Zuzana
    Charles Univ Prague, Fac Sci, Dept Analyt Chem, Prague 12843 2, Czech Republic.
    Bunikis, Ignas
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Carretero, Miguel A.
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal.
    Feiner, Nathalie
    Lund Univ, Dept Biol, S-22362 Lund, Sweden.
    Marsik, Petr
    Czech Univ Life Sci Prague, Fac Agrobiol Food & Nat Resources, Dept Food Sci, Prague 16521 6, Czech Republic.
    Pauperio, Francisco
    Univ Porto, Dept Biol, Fac Ciencias, P-4169007 Porto, Portugal.
    Salvi, Daniele
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal;Univ Aquila, Dept Hlth Life & Environm Sci, I-67100 Laquila, Italy.
    Soler, Lucile
    Natl Bioinformat Infrastruct Sweden, Sci Life Lab, S-75123 Uppsala, Sweden.
    While, Geoffrey M.
    Univ Tasmania, Sch ol Biol Sci, Hobart, Tas 7005, Australia;Univ Oxford, Dept Zool, Oxford OX1 3PS, England.
    Uller, Tobias
    Lund Univ, Dept Biol, S-22362 Lund, Sweden.
    Font, Enrique
    Univ Valencia, Cavanilles Inst Biodivers & Evolutionary Biol, Ethol Lab, Paterna 46980, Spain.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden;Texas A&M Univ, Coll Vet Med & Biomed Sci, Dept Vet Integrat Biosci, College Stn, TX 77843 USA.
    Carneiro, Miguel
    Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal;Univ Porto, Dept Biol, Fac Ciencias, P-4169007 Porto, Portugal.
    Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 12, p. 5633-5642Article in journal (Refereed)
    Abstract [en]

    Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.

  • 61.
    Andreasen, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Manktelow, Mariette
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sehic, Jasna
    Garkava-Gustavsson, Larisa
    Genetic identity of putative Linnaean plants: Successful DNA amplification of Linnaeus's crab apple Malus baccata2014In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 63, no 2, p. 408-416Article in journal (Other academic)
    Abstract [en]

    Advancements in molecular techniques enable us to extract DNA from historic herbarium specimens and facilitate genetic comparisons between herbarium material and living plant collections. These recent advances offer an exciting opportunity for identifying extant Linnaean plants by genetic comparisons of Linnaeus's own herbarium specimens with potentially remnant plants from his cultivations. DNA from the lectotype of Malus baccata (L.) Borkh. in the Linnaean Herbarium was successfully extracted and amplified for five of twelve loci of microsatellites. Results of genetic comparisons with M. baccata trees from Linnaeus's Hammarby, Sweden, show that the trees at Hammarby are closely related to each other, but not to the lectotype, which is closer to material from Russia. This suggests that Linnaeus received M. baccata from more than one source. Although not close to the lectotype and not represented by a specimen in the Linnaean Herbarium, the extant M. baccata at Hammarby may still represent Linnaean plants, that were grown by Linnaeus himself, or the descendants to such plants. Future studies on the almost 50 living, potential Linnaean plants may reveal an invaluable biological, scientific and cultural heritage from the era that saw the rise of systematic biology.

  • 62. Andres, J A
    et al.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Genetic divergence of the seminal signal-receptor system in houseflies: the footprints of sexually antagonistic coevolution?2001In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 268, no 1465, p. 399-405Article in journal (Refereed)
  • 63. Antoniazza, Sylvain
    et al.
    Burri, Reto
    Fumagalli, Luca
    Goudet, Jérôme
    Roulin, Alexandre
    Local adaptation maintains clinal variation in melanin-based coloration of European barn owls (Tyto alba).2010In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 64, no 7, p. 1944-1954Article in journal (Refereed)
    Abstract [en]

    Ecological parameters vary in space, and the resulting heterogeneity of selective forces can drive adaptive population divergence. Clinal variation represents a classical model to study the interplay of gene flow and selection in the dynamics of this local adaptation process. Although geographic variation in phenotypic traits in discrete populations could be remainders of past adaptation, maintenance of adaptive clinal variation requires recurrent selection. Clinal variation in genetically determined traits is generally attributed to adaptation of different genotypes to local conditions along an environmental gradient, although it can as well arise from neutral processes. Here, we investigated whether selection accounts for the strong clinal variation observed in a highly heritable pheomelanin-based color trait in the European barn owl by comparing spatial differentiation of color and of neutral genes among populations. Barn owl's coloration varies continuously from white in southwestern Europe to reddish-brown in northeastern Europe. A very low differentiation at neutral genetic markers suggests that substantial gene flow occurs among populations. The persistence of pronounced color differentiation despite this strong gene flow is consistent with the hypothesis that selection is the primary force maintaining color variation among European populations. Therefore, the color cline is most likely the result of local adaptation.

  • 64. Aplin, Lucy M.
    et al.
    Farine, Damien R.
    Morand-Ferron, Julie
    Cockburn, Andrew
    Thornton, Alex
    Sheldon, Ben C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Experimentally induced innovations lead to persistent culture via conformity in wild birds2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 518, no 7540, p. 538-541Article in journal (Refereed)
    Abstract [en]

    In human societies, cultural norms arise when behaviours are transmitted through social networks via high-fidelity social learning'. However, a paucity of experimental studies has meant that there is no comparable understanding of the process by which socially transmitted behaviours might spread and persist in animal populations'''. Here we show experimental evidence of the establishment of foraging traditions in a wild bird population. We introduced alternative novel foraging techniques into replicated wild sub-populations of great tits (Parus major) and used automated tracking to map the diffusion, establishment and long-term persistence of the seeded innovations. Furthermore, we used social network analysis to examine the social factors that influenced diffusion dynamics. From only two trained birds in each sub-population, the information spread rapidly through social network ties, to reach an average of 75% of individuals, with a total of 414 knowledgeable individuals performing 57,909 solutions over all replicates. The sub-populations were heavily biased towards using the technique that was originally introduced, resulting in established local traditions that were stable over two generations, despite a high population turnover. Finally, we demonstrate a strong effect of social conformity, with individuals disproportionately adopting the most frequent local variant when first acquiring an innovation, and continuing to favour social information over personal information. Cultural conformity is thought to be a key factor in the evolution of complex culture in humans''. In providing the first experimental demonstration of conformity in a wild non-primate, and of cultural norms in foraging techniques in any wild animal, our results suggest a much broader taxonomic occurrence of such an apparently complex cultural behaviour.

  • 65.
    Appelgren, Anais S. C.
    et al.
    Univ Bern, Inst Ecol & Evolut, Evolutionary Ecol Lab, Baltzerstr 6, Bern, Switzerland;Univ Lyon, CNRS, F-69000 Lyon, France;LBBE UMR 5558, Dept Biometry & Evolutionary Biol, Batiment Gregor Mendel,43 Blvd 11 Novembre 1918, F-69622 Villeurbanne, France;Univ Lyon 1, Dept Biometry & Evolutionary Biol, LBBE UMR 5558, Batiment Gregor Mendel,43 Blvd 11 Novembre 1918, F-69622 Villeurbanne, France;Univ Montpellier, Ctr IRD, Agropolis, MIVEGEC,CNRS,IRD, 911 Ave,BP 64501, F-34000 Montpellier, France.
    Saladin, Verena
    Univ Bern, Inst Ecol & Evolut, Evolutionary Ecol Lab, Baltzerstr 6, Bern, Switzerland.
    Richner, Heinz
    Univ Bern, Inst Ecol & Evolut, Evolutionary Ecol Lab, Baltzerstr 6, Bern, Switzerland.
    Doligez, Blandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lyon, CNRS, F-69000 Lyon, France;LBBE UMR 5558, Dept Biometry & Evolutionary Biol, Batiment Gregor Mendel,43 Blvd 11 Novembre 1918, F-69622 Villeurbanne, France;Univ Lyon 1, Dept Biometry & Evolutionary Biol, LBBE UMR 5558, Batiment Gregor Mendel,43 Blvd 11 Novembre 1918, F-69622 Villeurbanne, France.
    McCoy, Karen D.
    Univ Montpellier, Ctr IRD, Agropolis, MIVEGEC,CNRS,IRD, 911 Ave,BP 64501, F-34000 Montpellier, France.
    Gene flow and adaptive potential in a generalist ectoparasite2018In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 18, article id 99Article in journal (Refereed)
    Abstract [en]

    Background: In host-parasite systems, relative dispersal rates condition genetic novelty within populations and thus their adaptive potential. Knowledge of host and parasite dispersal rates can therefore help us to understand current interaction patterns in wild populations and why these patterns shift over time and space. For generalist parasites however, estimates of dispersal rates depend on both host range and the considered spatial scale. Here, we assess the relative contribution of these factors by studying the population genetic structure of a common avian ectoparasite, the hen flea Ceratophyllus gallinae, exploiting two hosts that are sympatric in our study population, the great tit Paws major and the collared flycatcher Ficedula albicollis. Previous experimental studies have indicated that the hen flea is both locally maladapted to great tit populations and composed of subpopulations specialized on the two host species, suggesting limited parasite dispersal in space and among hosts, and a potential interaction between these two structuring factors. Results: C gallinae fleas were sampled from old nests of the two passerine species in three replicate wood patches and were genotyped at microsatellite markers to assess population genetic structure at different scales (among individuals within a nest among nests and between host species within a patch and among patches). As expected, significant structure was found at all spatial scales and between host species, supporting the hypothesis of limited dispersal in this parasite. Clustering analyses and estimates of relatedness further suggested that inbreeding regularly occurs within nests. Patterns of isolation by distance within wood patches indicated that flea dispersal likely occurs in a stepwise manner among neighboring nests. From these data, we estimated that gene flow in the hen flea is approximately half that previously described for its great tit hosts. Conclusion: Our results fall in line with predictions based on observed patterns of adaptation in this host-parasite system, suggesting that parasite dispersal is limited and impacts its adaptive potential with respect to its hosts. More generally, this study sheds light on the complex interaction between parasite gene flow, local adaptation and host specialization within a single host-parasite system.

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  • 66.
    Arbuthnott, Devin
    et al.
    Univ British Columbia, Dept Zool, 4200-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.;Univ British Columbia, Biodivers Res Ctr, 4200-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada..
    Mautz, Brian S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rundle, Howard D.
    Univ Ottawa, Dept Biol, Ottawa, ON, Canada..
    Rugged fitness landscapes and by-product adaptation in experimental populations of Drosophila melanogaster2018In: Evolutionary Ecology Research, ISSN 1522-0613, E-ISSN 1937-3791, Vol. 19, no 1, p. 15-28Article in journal (Refereed)
    Abstract [en]

    Background: While the concept of the fitness landscape is central to evolutionary theory, empirical characterizations of fitness landscapes have remained difficult. Recently, a number of laboratory experiments using microbes have suggested that fitness landscapes are often rugged, though there is some variation across environments and species. However, there have been very few characterizations of fitness landscapes in sexual organisms, making it unclear whether the conclusions from studies of microbes are applicable to other groups. Questions: Are fitness landscapes smooth or rugged in simplified laboratory environments for sexual organisms? How does landscape topography influence patterns of adaptation? Methods: We conducted a series of experiments using replicate populations of Drosophila melanogaster adapted to either cadmium-or ethanol-enriched food to characterize the fitness and phenotypes of these populations in a simplified laboratory environment (ethanol-enriched media). Results: We found that replicate populations adapted to different laboratory environments have diverged phenotypically in physiology, mating behaviour, and offspring production in alternate environments. However, both ethanol-and cadmium-adapted populations show high fitness in the ethanol-enriched environment relative to their founding population, and cadmium-adapted males actually outcompete ethanol-adapted males for mates in an ethanol environment. Conclusions: Our data indicate that the simplified ethanol-enriched medium represents a rugged fitness landscape, and that alternately adapted populations occupy different fitness peaks on this landscape. Because cadmium-adapted populations were never exposed to ethanol previously, it appears that these populations adapted to ethanol as a by-product of adaptation to their cadmium-enriched environment. Therefore, even in simplified laboratory environments, we find evidence for rugged fitness landscapes, and the overlap of fitness peaks on the phenotypic landscape allowed for by-product adaptation.

  • 67.
    Arct, Aneta
    et al.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland.
    Drobniak, Szymon M.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland.
    Mellinger, Samantha
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cichon, Mariusz
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland.
    Parental genetic similarity and offspring performance in blue tits in relation to brood size manipulation2019In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, no 18, p. 10085-10091Article in journal (Refereed)
    Abstract [en]

    In birds, as in many other taxa, higher genetic similarity of mates has long been known to reduce offspring fitness. To date, the majority of avian studies have focused on examination whether the genetic similarity of social mates predicts hatching success. Yet, increased genetic similarity of mates may also reduce offspring fitness during later life stages, including the nestling period and beyond. Here, we investigated whether parental genetic similarity influences offspring performance using data from free-living blue tits (Cyanistes caeruleus) collected across three breeding seasons. Additionally, we tested whether brood size manipulation affects the magnitude and direction of the relationship between genetic similarity of mates and offspring performance. Sixteen microsatellite markers were used to measure genetic similarity between biological parents. We found that the genetic similarity of parents negatively affects offspring immune response and this effect was independent of the experimental brood size manipulation.

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  • 68.
    Arct, Aneta
    et al.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Sudyka, Joanna
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Podmoka, Edyta
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Drobniak, Szymon M.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cichon, Mariusz
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Heterozygosity-fitness correlations in blue tit nestlings (Cyanistis caeruleus) under contrasting rearing conditions2017In: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 31, no 5, p. 803-814Article in journal (Refereed)
    Abstract [en]

    Understanding the relation between genetic variation and fitness remains a key question in evolutionary biology. Although heterozygosity has been reported to correlate with many fitness-related traits, the strength of the heterozygosity-fitness correlations (HFCs) is usually weak and it is still difficult to assess the generality of these associations in natural populations. It has been suggested that HFCs may become meaningful only under particular environmental conditions. Moreover, existing evidence suggests that HFCs may also differ between sexes. The aim of this study was to investigate correlations between heterozygosity in neutral markers (microsatellites) and fitness-related traits in a natural population of blue tits (Cyanistes caeruleus). Additionally, we tested whether sex and environmental conditions may influence the magnitude and direction of HFCs. We found a positive relationship between heterozygosity and body mass of 14 days post-hatching nestlings, but only among females. Our results suggest that the correlation between heterozygosity and nestling body mass observed among female offspring could be attributed to within-brood effects. We failed to find any evidence that environmental conditions as simulated by brood size manipulation affect HFCs.

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  • 69. Arnegard, Matthew E.
    et al.
    McGee, Matthew D.
    Matthews, Blake
    Marchinko, Kerry B.
    Conte, Gina L.
    Kabir, Sahriar
    Bedford, Nicole
    Bergek, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Chan, Yingguang Frank
    Jones, Felicity C.
    Kingsley, David M.
    Peichel, Catherine L.
    Schluter, Dolph
    Genetics of ecological divergence during speciation2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 511, no 7509, p. 307-311Article in journal (Refereed)
    Abstract [en]

    Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.

  • 70.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Comparative evidence for the evolution of genitalia by sexual selection1998In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 393, no 6687, p. 784-786Article in journal (Refereed)
  • 71.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cryptic female choice2014In: The Evolution of Insect Mating Systems / [ed] D. Shuker and L. Simmons, Oxford: Oxford University Press, 2014, p. 204-220Chapter in book (Other academic)
  • 72.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Mixed Models Offer No Freedom from Degress Of Freedom2020In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 35, no 4, p. 329-335Article, review/survey (Refereed)
    Abstract [en]

    Statistics matter greatly in biology, whether we like it or not. As a discipline with an empirical inclination, we are faced with data every day and we rely on inferential statistical models to make sense of it and to provide us with novel insights. Much of the time, the growing level of complexity and sophistication of the models we put to use in ecology and evolution have led to more appropriate analyses of our data. However, this is not always the case. Here, I draw attention to a classic flaw in inferential statistics that has resurfaced in a new flavor as a result of increased reliance on complex linear mixed models -the multifaceted and disturbingly persistent problem of pseudoreplication.

  • 73.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    MULTIPLE MATING IN A WATER STRIDER - MUTUAL BENEFITS OR INTERSEXUAL CONFLICT1989In: Animal Behaviour, ISSN 0003-3472, E-ISSN 1095-8282, Vol. 38, p. 749-756Article in journal (Refereed)
  • 74.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sensory exploitation and sexual conflict2006In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 361, no 1466, p. 375-386Article in journal (Refereed)
  • 75.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sex wars: Genes, bacteria, and biased sex ratios2003In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 424, no 6949, p. 616-617Article in journal (Refereed)
  • 76.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sexual conflict and sexual selection: Lost in the chase2004In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 58, no 6, p. 1383-1388Article in journal (Refereed)
  • 77.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Andres, Jose A.
    The effects of experimentally induced polyandry on female reproduction in a monandrous mating system2006In: Ethology, ISSN 0179-1613, E-ISSN 1439-0310, Vol. 112, no 8, p. 748-756Article in journal (Refereed)
  • 78.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Danielsson, I
    Copulatory behavior, genital morphology, and male fertilization success in water striders1999In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 53, no 1, p. 147-156Article in journal (Refereed)
  • 79.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Danielsson, I
    Postmating sexual selection: the effects of male body size and recovery period on paternity and egg production rate in a water strider1999In: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 10, no 4, p. 358-365Article in journal (Refereed)
  • 80.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Edvardsson, M
    Friberg, U
    Nilsson, T
    Sexual conflict promotes speciation in insects2000In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 97, no 19, p. 10460-10464Article in journal (Refereed)
  • 81.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Fricke, C
    Arnqvist, G
    Patterns of divergence in the effects of mating on female reproductive performance in flour beetles2002In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 56, no 1, p. 111-120Article in journal (Refereed)
  • 82.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Johansson, F
    Ontogenetic reaction norms of predator-induced defensive morphology in dragonfly larvae1998In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 79, no 6, p. 1847-1858Article in journal (Refereed)
  • 83.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jones, T M
    Elgar, M A
    Insect behaviour: Reversal of sex roles in nuptial feeding2003In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 424, no 6947, p. 387-387Article in journal (Refereed)
  • 84.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kirkpatrick, M
    The evolution of infidelity in socially monogamous passerines: The strength of direct and indirect selection on extrapair copulation behavior in females2005In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 165, no 5, p. S26-S37Article in journal (Refereed)
  • 85.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Martensson, T
    Measurement error in geometric morphometrics: Empirical strategies to assess and reduce its impact on measures of shape1998In: Acta Zoologica Academiae Scientiarum Hungaricae, ISSN 1217-8837, E-ISSN 2064-2474, Vol. 44, no 1-2, p. 73-96Article in journal (Refereed)
  • 86.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Nilsson, T
    The evolution of polyandry: multiple mating and female fitness in insects2000In: Animal Behaviour, ISSN 0003-3472, E-ISSN 1095-8282, Vol. 60, p. 145-164Article, review/survey (Refereed)
  • 87.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Nilsson, T
    Katvala, M
    Mating rate and fitness in female bean weevils2005In: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 16, no 1, p. 123-127Article in journal (Refereed)
  • 88.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rowe, L
    Antagonistic coevolution between the sexes in a group of insects2002In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 415, no 6873, p. 787-789Article in journal (Refereed)
  • 89.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rowe, L
    Correlated evolution of male and female morphologies in water striders2002In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 56, no 5, p. 936-947Article in journal (Refereed)
  • 90.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sayadi, Ahmed
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Immonen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hotzy, Cosima
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rankin, Daniel
    Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland..
    Tuda, Midori
    Kyushu Univ, Dept Bioresource Sci, Lab Insect Nat Enemies, Fukuoka 8128581, Japan.;Kyushu Univ, Inst Biol Control, Fac Agr, Fukuoka 8128581, Japan..
    Hjelmen, Carl E.
    Texas A&M Univ, Dept Entomol, College Stn, TX 77843 USA..
    Johnston, J. Spencer
    Texas A&M Univ, Dept Entomol, College Stn, TX 77843 USA..
    Genome size correlates with reproductive fitness in seed beetles2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1815, article id 20151421Article in journal (Refereed)
    Abstract [en]

    The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the 'C-value paradox'. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4-5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution.

  • 91.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Stojkovic, Biljana
    Department of Evolutionary Biology, Institute for Biological Research, University of Belgrade, Belgrade, Serbia.; Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia.
    Rönn, Johanna L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Immonen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    The pace-of-life: A sex-specific link between metabolic rate and life history in bean beetles2017In: Functional Ecology, ISSN 0269-8463, E-ISSN 1365-2435, Vol. 31, no 12, p. 2299-2309Article in journal (Refereed)
    Abstract [en]
    1. Metabolic rate (MR) is a key functional trait simply because metabolism converts resources into population growth rate. Yet, our empirical understanding of the sources of within species variation in MR, as well as of its life history and ecological correlates, is rather limited. Here, we assess whether MR lies at the root of a syndrome of correlated rate-dependent life-history traits in an insect.
    2. Selection for early (E) or late (L) age-at-reproduction for >160 generations in the bean beetle Acanthoscelides obtectus has produced beetles that differ markedly in juvenile development, body size, fecundity schedules, ageing and life span. Here, we use micro-respirometry to test whether this has been associated with the evolution of age- and sex-specific metabolic phenotypes.
    3. We find that mass-specific MR is 18% higher in E lines compared to L lines and that MR decreases more rapidly with chronological, but not biological, age in E lines. Males, under sexual selection to “live-fast-die-young”, show 50% higher MR than females and MR decreased more rapidly with age in males.
    4. Our results are consistent with a central role for MR for the divergence in “pace-of-life” seen in these beetles, supporting the view that MR lies at the root of ecologically relevant life-history trait variation within species.
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  • 92.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Thornhill, R
    Evolution of animal genitalia: patterns of phenotypic and genotypic variation and condition dependence of genital and non-genital morphology in water strider (Heteroptera : Gerridae : Insecta)1998In: Genetical Research, ISSN 0016-6723, E-ISSN 1469-5073, Vol. 71, no 3, p. 193-212Article in journal (Refereed)
  • 93.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Vellnow, Nikolas
    Rowe, Locke
    The effect of epistasis on sexually antagonistic genetic variation2014In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, no 1787, p. 20140489-Article in journal (Refereed)
    Abstract [en]

    There is increasing evidence of segregating sexually antagonistic (SA) genetic variation for fitness in laboratory and wild populations, yet the conditions for the maintenance of such variation can be restrictive. Epistatic interactions between genes can contribute to the maintenance of genetic variance in fitness and we suggest that epistasis between SA genes should be pervasive. Here, we explore its effect on SA genetic variation in fitness using a two locus model with negative epistasis. Our results demonstrate that epistasis often increases the parameter space showing polymorphism for SA loci. This is because selection in one locus is affected by allele frequencies at the other, which can act to balance net selection in males and females. Increased linkage between SA loci had more marginal effects. We also show that under some conditions, large portions of the parameter space evolve to a state where male benefit alleles are fixed at one locus and female benefit alleles at the other. This novel effect of epistasis on SA loci, which we term the 'equity effect', may have important effects on population differentiation and may contribute to speciation. More generally, these results support the suggestion that epistasis contributes to population divergence.

  • 94.
    Ast, Jennifer C
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Mitochondrial DNA evidence and evolution in Varanoidea (Squamata)2001In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 17, no 3, p. 211-226Article in journal (Refereed)
    Abstract [en]

    Varanoidea is a monophyletic group of anguimorph lizards, comprising the New World helodermatids, the Bornean earless monitor Lanthanotus borneensis, and the Old World monitors (Varanus). I use mitochondrial DNA sequences and extensive taxonomic sampling to test alternative hypotheses of varanoid relationships. The most parsimonious hypothesis confirms the monophyly of Varanoidea (Heloderma, Lanthanotus, and Varanus) and Varanus, as well as the sister-taxon relationship of Varanus and Lanthanotus. The relationships among Varanus species differ in several respects from previous hypotheses. Three major lineages are recognized within Varanus: an African clade basal to the rest of the group, an Indo-Asian clade, and an Indo-Australian clade. Within the last lineage, the endemic Australian dwarf monitors (Odatria) form a clade sister to the large Australian monitors (the gouldii group). Tests of the effects of rate heterogeneity and homoplasy demonstrate that putative process partitions of data are largely congruent with one another and contribute positive support to the overall hypothesis.

  • 95.
    Augusto, Rafael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Assortative reproduction in a seed beetle?2016Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    How genetic variation for fitness is maintained is still debated in evolutionary biology. Sexually antagonistic (SA) selection, favouring alternative alleles in males and females, has been proposed to be one mechanism capable of maintaining genetic variation for fitness. However the conditions under which SA polymorphisms are maintained are still thought to be somewhat restrictive. Several models have explored potential mechanisms that may help maintain genetic variation at SA loci. One such mechanism is assortative mating by fitness, where individuals with similar fitness mate more frequently than expected by random chance. This study explores if there is such assortative reproduction for fitness in a population of Callosobruchus maculatus seed beetles, which could explain the large amounts of SA genetic variance for fitness exhibited by this population. However, on the contrary, results show that there is evidence of disassortative reproduction for fitness in this population. 

  • 96. Axelsson, Erik
    Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and Turkey2004In: Mol Biol Evol.Article in journal (Refereed)
  • 97. Axelsson, Erik
    et al.
    Webster, Matthew
    Base Composition Patterns2011In: Encyclopedia of Life Sciences, ISSN 1561592617 9781561592616Article, book review (Refereed)
  • 98. Axelsson, Erik
    et al.
    Willerslev, Eske
    Gilbert, M Thomas P
    Nielsen, Rasmus
    The effect of ancient DNA damage on inferences of demographic histories.2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 10, p. 2181-7Article in journal (Refereed)
    Abstract [en]

    The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.

  • 99.
    Babiker, Hiba
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schlebusch, Carina M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hassan, Hisham Y
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci.2011In: Investigative Genetics, ISSN 2041-2223, E-ISSN 2041-2223, Vol. 2, no 1Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.

    RESULT: We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.

    CONCLUSION: We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

  • 100.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Adaptive evolution in passerine birds2014In: Encyclopedia of Life Sciences, ISSN 1476-9506, E-ISSN 1476-9506Article in journal (Other academic)
    Abstract [en]

    Adaptive evolution is the process whereby mutations that provide the carrier with a selective advantage increase in frequency in a population via the process of natural selection. Passerines are widespread, common and long-term targets for field study and they demonstrate a copious diversity in physiological and morphological adaptations to varying habitats, for example, beak size and wing shape, and they are, therefore, an important study system to understand adaptive evolution. Recent technological advancements have made it easier to investigate the mechanistic and evolutionary underpinnings of adaptive evolution by allowing genome sequence data to be generated in almost any species of interest. However, it is important to assess the contribution of neutral forces like demographic events and GC-biased gene conversion before concluding that selection has shaped the patterns observed in genomic data. Initial analyses in passerines have identified candidate genes that might be involved in, for example, song learning, beak morphology, disease resistance, high-altitude adaptation and exploratory behavior, but functional verifications are needed to establish a causative relationship between the identified genes and the traits. Key Concepts:Key Concepts: * Passerines are widespread, generally common and easy targets for field study and they demonstrate a copious diversity in physiological and morphological adaptations to varying habitats and they have, therefore, played an important role in previous studies concerning behaviour, ecology and evolution. * A full understanding of passerine adaptations requires an integrative approach aiming at identifying and characterising both proximate (mechanistic) and ultimate (evolutionary) underpinnings to adaptive traits. * The recent advancements in molecular techniques allows for using both comparative genomics, expression profiling, candidate gene approaches and classical association and QTL mapping strategies to identify the genetic basis of adaptive traits in passerines. * Groundwork studies of ecological genetics and genomics using comparative approaches, expression profiling and candidate genes are now accumulating and in a handful of cases we have an idea about the genetic basis of adaptive traits related to, for example, dietary specialisation, learning, exploratory behaviour, immune response and high-altitude adaptations in passerines. * Demographic history and other neutral processes, for example, GC-biased gene conversion (gcBGC), may mimic signals of selection and it is important to verify findings of adaptive evolution using independent methods.

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