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  • 1551.
    Stewart, Joshua D.
    et al.
    University of California, USA ; The Manta Trust, UK.
    Beale, Calvin S.
    Misool Manta Project, Indonesia.
    Fernando, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). The Manta Trust, UK ; Blue Resources, Sri Lanka.
    Sianipar, Abraham B.
    Conservation International, Indonesia.
    Burton, Ronald S.
    University of California, USA.
    Semmens, Brice X.
    University of California, USA.
    Aburto-Oropeza, Octavio
    University of California, USA.
    Spatial ecology and conservation of Manta birostris in the Indo-Pacific2016Inngår i: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 200, s. 178-183Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Information on the movements and population connectivity of the oceanic manta ray (Manta birostris) is scarce. The species has been anecdotally classified as a highly migratory species based on the pelagic habitats it often occupies, and migratory behavior exhibited by similar species. As a result, in the absence of ecological data, population declines in oceanic manta have been addressed primarily with international-scale management and conservation efforts. Using a combination of satellite telemetry, stable isotope and genetic analyses we demonstrate that, contrary to previous assumptions, the species appears to exhibit restricted movements and fine-scale population structure. M. birostris tagged at four sites in the Indo-Pacific exhibited no long-range migratory movements and had non-overlapping geographic ranges. Using genetic and isotopic analysis, we demonstrate that the observed movements and population structure persist on multi-year and generational time scales. These data provide the first insights into the long-term movements and population structure of oceanic manta rays, and suggest that bottom-up, local or regional approaches to managing oceanic mantas could prove more effective than existing, international-scale management strategies. This case study highlights the importance of matching the scales at which management and relevant ecological processes occur to facilitate the effective conservation of threatened species.

  • 1552.
    Stocks, Michael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Neutral and Adaptive Processes Shaping Genetic Variation in Spruce Species2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Population genetic analyses can provide information about both neutral and selective evolutionary processes shaping genetic variation. In this thesis, extensive population genetic methods were used to make inferences about genetic drift and selection in spruce species. In paper I we studied four species from the Qinghai-Tibetan Plateau (QTP): Picea likiangensis, P. purpurea, P. wilsonii and P. schrenkiana. Big differences in estimates of genetic diversity and Ne were observed in the more restricted species, P. schrenkiana, and the other more widely distributed species. Furthermore, P. purpurea appears to be a hybrid between P. likiangensis and P. wilsonii. In paper II we used Approximate Bayesian Computation (ABC) to find that the data support a drastic reduction of Ne in Taiwan spruce around 300-500 kya, in line with evidence from the pollen records. The split from P. wilsonii was dated to between 4-8 mya, around the time that Taiwan was formed. These analyses relied on a small sample size, and so in Paper III we investigated the impact of small datasets on the power to distinguish between models in ABC. We found that when genetic diversity is low there is little power to distinguish between simple coalescent models and this can determine the number of samples and loci required.

    In paper IV we studied the relative importance of genetic drift and selection in four spruce species with differing Ne: P. abies, P. glauca, P. jezoensis and P. breweriana. P. breweriana, which has a low Ne, exhibits a low fraction of adaptive substitutions, while P. abies has high Ne and a high fraction of adaptive substitutions. The other two spruce, however, do not support this suggesting other factors a more important. In paper V we find that several SNPs correlate with both a key adaptive trait (budset) and latitude. The expression of one in particular (PoFTL2) correlates with budset and was previously indentified in P. abies. These studies have helped characterise the importance of different population genetic processes in shaping genetic variation in spruce species and has laid some solid groundwork for future studies of spruce.

  • 1553.
    Stocks, Michael
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Chen, Jun
    Institut fur Populationsgenetik, Wien.
    Källman, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Bousquet, Jean
    Universite Laval, Quebec.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Molecular adaptation in spruce speciesManuskript (preprint) (Annet vitenskapelig)
  • 1554.
    Stocks, Michael
    et al.
    University of Sheffield, Sheffield, United Kingdom; Department of Plant Ecology and Evolution, Uppsala University, Uppsala, Sweden.
    Dean, Rebecca
    Uppsala University, Uppsala, Sweden; Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
    Rogell, Björn
    Department of Animal Ecology, Uppsala University, Uppsala, Sweden; Department of Zoology, Stockholm University, Stockholm, Sweden.
    Friberg, Urban
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan. Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
    Sex-specific Trans-regulatory Variation on the Drosophila melanogaster X Chromosome2015Inngår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, nr 2, s. 1-19, artikkel-id e1005015Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The X chromosome constitutes a unique genomic environment because it is present in onecopy in males, but two copies in females. This simple fact has motivated several theoreticalpredictions with respect to how standing genetic variation on the X chromosome should differfrom the autosomes. Unmasked expression of deleterious mutations in males and alower census size are expected to reduce variation, while allelic variants with sexually antagonisticeffects, and potentially those with a sex-specific effect, could accumulate on theX chromosome and contribute to increased genetic variation. In addition, incomplete dosagecompensation of the X chromosome could potentially dampen the male-specific effectsof random mutations, and promote the accumulation of X-linked alleles with sexually dimorphicphenotypic effects. Here we test both the amount and the type of genetic variation onthe X chromosome within a population of Drosophila melanogaster, by comparing the proportionof X linked and autosomal trans-regulatory SNPs with a sexually concordant anddiscordant effect on gene expression. We find that the X chromosome is depleted for SNPswith a sexually concordant effect, but hosts comparatively more SNPs with a sexually discordanteffect. Interestingly, the contrasting results for SNPs with sexually concordant anddiscordant effects are driven by SNPs with a larger influence on expression in females thanexpression in males. Furthermore, the distribution of these SNPs is shifted towards regionswhere dosage compensation is predicted to be less complete. These results suggest thatintrinsic properties of dosage compensation influence either the accumulation of differenttypes of trans-factors and/or their propensity to accumulate mutations. Our findings documenta potential mechanistic basis for sex-specific genetic variation, and identify the X as areservoir for sexually dimorphic phenotypic variation. These results have general implicationsfor X chromosome evolution, as well as the genetic basis of sex-specificevolutionary change.

  • 1555.
    Stocks, Michael
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Siol, Mathieu
    Institut National de la Recherche Agronomique (INRA), UMR Agroecologie, Dijon.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    De Mita, Stéphane
    Institut National de la Recherche Agronomique (INRA), UMR Interactions Arbres-Microorganismes, Nancy.
    Amount of information needed for model choice in Approximate Bayesian Computation2014Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 6, s. e99581-Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study.

  • 1556.
    Strand, Tanja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    European Black Grouse: MHC Genetic Diversity and Population Structure2011Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Black grouse Tetrao tetrix is a bird species composed of large, continuous as well as severely reduced and fragmented populations, making it an optimal species to investigate how genetic diversity is affected by habitat fragmentation. I have focused on genetic diversity in the Major Histocompatibility Complex (MHC) to measure the ability of the black grouse to respond to environmental changes.

    I partly characterized MHC class II in black grouse and found striking similarities with chicken MHC class II. I demonstrated that black grouse possess a similar compact MHC as chicken with few MHC class II B (BLB) and Y (YLB) loci. I did not find evidence of balancing selection in YLB so I concentrated further studies on BLB.

    I developed a PCR-based screening method for amplifying and separating expressed BLB alleles in European black grouse populations. Small fragmented populations had lost neutral genetic diversity (based on microsatellites and SNPs) compared to samples from the historical distribution and contemporary large populations. There was also a trend, albeit less pronounced, for reduced MHC diversity in these populations. Neutral markers in small isolated populations were affected by increased levels of genetic drift and were therefore genetically differentiated compared to other populations. MHC markers on the other hand, were not subjected to genetic drift to the same extent probably due a long historic process of balancing selection.

    Inferences of heterozygosity and evolutionary patterns as well as detailed correlations to reproductive success and diseases cannot be performed until MHC can be amplified in a locus-specific manner. Therefore, I developed a single locus sequence-based typing method for independently amplifying MHC class II B loci (BLB1 and BLB2). I found that BLB1 and BLB2 were duplicated in a common ancestor to chickens and black grouse and that these loci are subjected to homogenizing concerted evolution due to inter-genetic exchange between loci after species divergence.  I could also verify that both BLB1 and BLB2 were transcribed in black grouse and under balancing selection.

    This collection of work has significance for future conservation of black grouse as well as research and management of zoonotic diseases.

  • 1557.
    Strand, Tanja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Segelbacher, Gernot
    Dept Wildlife Ecology and Management, University Freiburg.
    Quintela, Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña.
    Xiao, Lyngyun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Axelsson, Tomas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?2012Inngår i: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 2, nr 2, s. 341-353Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here we use both neutral and MHC markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled eleven different populations; five continuous, three isolated and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 SNPs (Single Nucleotide Polymorphisms) which both were found to be neutral, and two functional MHC (Major Histocompatibility Complex) genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented. 

  • 1558.
    Strand, Tanja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Wang, Biao
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Meyer-Lucht, Yvonne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Evolutionary history of black grouse BLB1 and BLB2 revealed through single locus sequence-based typingManuskript (preprint) (Annet vitenskapelig)
  • 1559.
    Strand, Tanja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Westerdahl, Helena
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Alatalo, Rauno V.
    Siitari, Heli
    The MHC class II of the Black grouse (Tetrao tetrix) consists of low numbers of B and Y genes with variable diversity and expression2007Inngår i: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 59, nr 9, s. 725-734Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We found that the Black grouse (Tetrao tetrix) possess low numbers of Mhc class II B (BLB) and Y (YLB) genes with variable diversity and expression. We have therefore shown, for the first time, that another bird species (in this case, a wild lek-breeding galliform) shares several features of the simple Mhc of the domestic chicken (Gallus gallus). The Black grouse BLB genes showed the same level of polymorphism that has been reported in chicken, and we also found indications of balancing selection in the peptide-binding regions. The YLB genes were less variable than the BLB genes, also in accordance with earlier studies in chicken, although their functional significance still remains obscure. We hypothesize that the YLB genes could have been under purifying selection, just as the mammal Mhc-E gene cluster.

  • 1560.
    Strassert, Jürgen F H
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
    Karnkowska, Anna
    Hehenberger, Elisabeth
    del Campo, Javier
    Kolisko, Martin
    Okamot, Noriko
    Burki, Fabien
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
    Janouškovec, Jan
    Poirier, Camille
    Leonard, Guy
    Hallam, Steven J
    Richards, Thomas A
    Worden, Alexandra Z
    Santoro, Alyson E
    Keeling, Patrick J
    Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates2018Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, s. 304-308Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.

  • 1561.
    Strese, Ake
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi.
    Backlund, Anders
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi.
    Alsmark, Cecilia
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi.
    A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes2014Inngår i: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 14, s. 119-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results: A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions: We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.

  • 1562.
    Strimling, Pontus
    et al.
    Stockholms universitet, Humanistiska fakulteten, Centrum för evolutionär kulturforskning.
    Sjöstrand, Jonas
    Stockholms universitet, Humanistiska fakulteten, Centrum för evolutionär kulturforskning.
    Enquist, Magnus
    Stockholms universitet, Humanistiska fakulteten, Centrum för evolutionär kulturforskning. Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Eriksson, Kimmo
    Stockholms universitet, Humanistiska fakulteten, Centrum för evolutionär kulturforskning.
    Accumulation of independent cultural traits2009Inngår i: Theoretical Population Biology, ISSN 0040-5809, E-ISSN 1096-0325, Vol. 76, nr 2, s. 77-83Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In a species capable of (imperfect) social learning, how much culture can a population of a given size carry? And what is the relationship between the individual and the population? In the first study of these novel questions, here we develop a mathematical model of the accumulation of independent cultural traits in a finite population with overlapping generations.

  • 1563.
    Stångberg, Josefine
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    The evolution of sexual dimorphism in life history traits2017Rapport (Annet vitenskapelig)
    Abstract [en]

    Many dioecious organisms exhibit some level of sexual dimorphism; the sexes can differ in phenotype, and can have different fitness optima for certain traits and have different reproductive strategies. Sex-specific selection, thus, can be highly diverging in both magnitude and direction. When selection for a trait differs in direction we have antagonistic selection; this often leads to sexual conflicts since the two sexes share most of their genetic architecture. Sexual dimorphism is often seen as a resolution to sexual conflict, a way to decouple the genetic basis of traits under conflict and allow sex-specific expression. One way to better understand the evolution of sexual dimorphism is using a life history theory framework; where traits linked to growth, reproduction and survival are studied and quantified. These quantitative traits, their genetic architecture and how they covary within and between the two sexes, can be further studied using a quantitative genetics approach – G and B matrices. These are essentially genetic variance-covariance matrices of all traits measured, pairwise comparisons that give a picture of how these traits coevolve within an individual (G), but also how different traits covary between the sexes (B). These tools allow us to understand the underlying genetic architecture of life history traits, and also how these traits change under different and sex-specific selection pressures. This, in turn, will aid our understanding of how sexual dimorphism evolves. I end this review by focusing on a particular model species for studying these questions; the nematode Caenorhabditis remanei. 

  • 1564. Sudyka, J.
    et al.
    Arct, A.
    Drobniak, S.
    Dubiec, A.
    Gustafsson, Lars
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Cichon, M.
    Experimentally increased reproductive effort alters telomere length in the blue tit (Cyanistes caeruleus)2014Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, nr 10, s. 2258-2264Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Telomeres have recently been suggested to play important role in ageing and are considered to be a reliable ageing biomarkers. The life history theory predicts that costs of reproduction should be expressed in terms of accelerated senescence, and some empirical studies do confirm such presumption. Thus, a link between reproductive effort and telomere dynamics should be anticipated. Recent studies have indeed demonstrated that reproduction may trigger telomere loss, but actual impact of reproductive effort has not received adequate attention in experimental studies. Here, we experimentally manipulated reproductive effort by increasing the brood size in the wild blue tit (Cyanistes caeruleus). We show that parents attending enlarged broods experienced larger yearly telomere decay in comparison to control birds attending unaltered broods. In addition, we demonstrate that the change in telomere length differs between sexes, but this effect was independent from our treatment. To our knowledge, this is the first experimental study in the wild revealing that telomere dynamics may be linked to reproductive effort. Thus, telomere shortening may constitute one of the potential proximate mechanisms mediating the costs of reproduction.

  • 1565.
    Sudyka, Joanna
    et al.
    Univ Warsaw, Ctr New Technol, Banacha 2c, PL-02097 Warsaw, Poland;Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland.
    Podmokla, 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.
    Dubiec, Anna
    Polish Acad Sci, Museum & Inst Zool, Ul Wilcza 64, PL-00679 Warsaw, Poland.
    Arct, Aneta
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland.
    Gustafsson, Lars
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Cichon, Mariusz
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland.
    Sex-specific effects of parasites on telomere dynamics in a short-lived passerinethe blue tit2019Inngår i: The Science of Nature: Naturwissenschaften, ISSN 0028-1042, E-ISSN 1432-1904, Vol. 106, nr 1-2, artikkel-id 6Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Parasitic infections potentially drive host's life-histories since they can have detrimental effects on host's fitness. Telomere dynamics is a candidate mechanism to underlie life-history trade-offs and as such may correlate with observed fitness reduction in infected animals. We examined the relationship of chronic infection with two genera of haemosporidians causing avian malaria and malaria-like disease with host's telomere length (TL) in a longitudinal study of free-ranging blue tits. The observed overall infection prevalence was 80% and increased with age, constituting a potentially serious selective pressure in our population. We found longer telomeres in individuals infected with a parasite causing lesser blood pathologies i.e. Haemoproteus compared to Plasmodium genus, but this only held true among males. Female TL was independent of the infection type. Our results indicate that parasitic infections could bring about other types of costs to females than to males with respect to TL. Additionally, we detected linear telomere loss with age, however a random regression analysis did not confirm significant heterogeneity in TL of first breeders and telomere shortening rates in further life.

  • 1566.
    Suh, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves2016Inngår i: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 45, s. 50-62Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Birds have arguably been the most intensely studied animal group for their phylogenetic relationships. However, the recent advent of genome-scale phylogenomics has made the forest of bird phylogenies even more complex and confusing. Here, in this perspective piece, I show that most parts of the avian Tree of Life are now firmly established as reproducible phylogenetic hypotheses. This is to the exception of the deepest relationships among Neoaves. Using phylogenetic networks and simulations, I argue that the very onset of the super-rapid neoavian radiation is irresolvable because of eight near-simultaneous speciation events. Such a hard polytomy of nine taxa translates into 2 027 025 possible rooted bifurcating trees. Accordingly, recent genome-scale phylogenies show extremely complex conflicts in this (and only this) part of the avian Tree of Life. I predict that the upcoming years of avian phylogenomics will witness many more, highly conflicting tree topologies regarding the early neoavian polytomy. I further caution against bootstrapping in the era of genomics and suggest to instead use reproducibility (e.g. independent methods or data types) as support for phylogenetic hypotheses. The early neoavian polytomy coincides with the Cretaceous-Paleogene (K-Pg) mass extinction and is, to my knowledge, the first empirical example of a hard polytomy.

  • 1567.
    Suh, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The Specific Requirements for CR1 Retrotransposition Explain the Scarcity of Retrogenes in Birds2015Inngår i: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 81, nr 1-2, s. 18-20Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chicken repeat 1 (CR1) retroposons are the most abundant superfamily of transposable elements in the genomes of birds, crocodilians, and turtles. However, CR1 mobilization remains poorly understood. In this article, I document that the diverse CR1 lineages of land vertebrates share a highly conserved hairpin structure and an octamer microsatellite motif at their very 3' ends. Together with the presence of these same motifs in the tails of CR1-mobilized short interspersed elements, this suggests that the minimum requirement for CR1 transcript recognition and retrotransposition is a complex > 50-nt structure. Such a highly specific recognition sequence readily explains why CR1-dominated genomes generally contain very few retrogenes. Conversely, the mammalian richness in retrogenes results from CR1 extinction in their early evolution and subsequent establishment of L1 dominance.

  • 1568.
    Suh, Alexander
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. University of Münster, Institute of Experimental Pathology (ZMBE).
    Bachg, Sandra
    University of Münster, Institute of Experimental Pathology (ZMBE).
    Donnellan, Stephen
    South Australian Museum, Adelaide; The University of Adelaide, School of Biological Sciences.
    Joseph, Leo
    National Research Collections Australia, CSIRO, Australian National Wildlife Collection.
    Brosius, Jürgen
    University of Münster, Institute of Experimental Pathology (ZMBE); Brandenburg Medical School (MHB).
    Kriegs, Jan Ole
    University of Münster, Institute of Experimental Pathology (ZMBE); Westfälisches Landesmuseum mit Planetarium, LWL-Museum für Naturkunde.
    Schmitz, Jürgen
    University of Münster, Institute of Experimental Pathology (ZMBE).
    De-novo emergence of SINE retroposons during the early evolution of passerine birds2017Inngår i: Mobile DNA, ISSN 1759-8753, E-ISSN 1759-8753, Vol. 8, artikkel-id 21Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes.

    Results: Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri - songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching.

    Conclusions: We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.

  • 1569.
    Suh, Alexander
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Churakov, Gennady
    Ramakodi, Meganathan P.
    Platt, Roy N., II
    Jurka, Jerzy
    Kojima, Kenji K.
    Caballero, Juan
    Smit, Arian F.
    Vliet, Kent A.
    Hoffmann, Federico G.
    Brosius, Juergen
    Green, Richard E.
    Braun, Edward L.
    Ray, David A.
    Schmitz, Juergen
    Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes2015Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 7, nr 1, s. 205-217Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.

  • 1570.
    Suh, Alexander
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Smeds, Linnea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes2018Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, nr 1, s. 99-111Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Transposable elements (TEs) are genomic parasites capable of inserting virtually anywhere in the host genome, with manifold consequences for gene expression, DNA methylation and genomic stability. Notably, they can contribute to phenotypic variation and hence be associated with, for example, local adaptation and speciation. However, some organisms such as birds have been widely noted for the low densities of TEs in their genomes and this has been attributed to a potential dearth in transposition during their evolution. Here, we show that avian evolution witnessed diverse and abundant transposition on very recent timescales. First, we made an in-depth repeat annotation of the collared flycatcher genome, including identification of 23 new, retrovirus-like LTR retrotransposon families. Then, using whole-genome resequencing data from 200 Ficedula flycatchers, we detected 11,888 polymorphic TE insertions (TE presence/absence variations, TEVs) that segregated within and among species. The density of TEVs was one every 1.5-2.5Mb per individual, with heterozygosities of 0.12-0.16. The majority of TEVs belonged to some 10 different LTR families, most of which are specific to the flycatcher lineage. TEVs were validated by tracing the segregation of hundreds of TEVs across a three-generation pedigree of collared flycatchers and also by their utility as markers recapitulating the phylogenetic relationships among flycatcher species. Our results suggest frequent germline invasions of songbird genomes by novel retroviruses as a rich source of structural variation, which may have had underappreciated phenotypic consequences for the diversification of this species-rich group of birds.

  • 1571.
    Suh, Alexander
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Smeds, Linnea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds2015Inngår i: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 13, nr 8, artikkel-id e1002224Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS), i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree.

  • 1572.
    Suh, Alexander
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Witt, Christopher C.
    Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA.;Univ New Mexico, Museum Southwestern Biol, Albuquerque, NM 87131 USA..
    Menger, Juliana
    UFZ Helmholtz Ctr Environm Res, Dept Conservat Biol, D-04318 Leipzig, Germany.;Univ Leipzig, Inst Biol, Mol Evolut & Systemat Anim, D-04103 Leipzig, Germany.;INPA, BR-69067375 Manaus, Amazonas, Brazil..
    Sadanandan, Keren R.
    Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore..
    Podsiadlowski, Lars
    Univ Bonn, Inst Evolutionary Biol & Ecol, D-53121 Bonn, Germany..
    Gerth, Michael
    Univ Leipzig, Inst Biol, Mol Evolut & Systemat Anim, D-04103 Leipzig, Germany.;Univ Liverpool, Inst Integrat Biol, Liverpool L69 7ZB, Merseyside, England..
    Weigert, Anne
    Univ Leipzig, Inst Biol, Mol Evolut & Systemat Anim, D-04103 Leipzig, Germany.;Max Planck Inst Evolutionary Anthropol, D-04103 Leipzig, Germany..
    McGuire, Jimmy A.
    Univ Calif Berkeley, Museum Vertebrate Zool, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Mudge, Joann
    Natl Ctr Genome Resources, Santa Fe, NM 87505 USA..
    Edwards, Scott V.
    Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA..
    Rheindt, Frank E.
    Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore..
    Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes2016Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, artikkel-id 11396Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83-99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25-22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20-17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity.

  • 1573.
    Sulej, Tomasz
    et al.
    PAS, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    An elephant-sized Late Triassic synapsid with erect limbs2019Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 363, nr 6422, s. 78-80Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Here, we describe the dicynodont Lisowicia bojani, from the Late Triassic of Poland, a gigantic synapsid with seemingly upright subcursorial limbs that reached an estimated length of more than 4.5 meters, height of 2.6 meters, and body mass of 9 tons. Lisowicia is the youngest undisputed dicynodont and the largest nondinosaurian terrestrial tetrapod from the Triassic. The lack of lines of arrested growth and the highly remodeled cortex of its limb bones suggest permanently rapid growth and recalls that of dinosaurs and mammals. The discovery of Lisowicia overturns the established picture of the Triassic megaherbivore radiation as a phenomenon restricted to dinosaurs and shows that stem-group mammals were capable of reaching body sizes that were not attained again in mammalian evolution until the latest Eocene.

  • 1574.
    Sun, Yu
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Genome Evolution of Neurospora tetrasperma2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In this thesis work, I have used a comparative genomics approach to study a fungal model organism, Neurospora tetrasperma. My specific focus has been on genomic introgression, intron evolution, chromosomal structural rearrangements and codon usage. All of the studies are based on large-scale dataset generated by next-generation sequencing technology (NGS), combined with other techniques, such as Optical Mapping. In the introgression study, we detected large-scale introgression tracts in three N. tetrasperma lineages, and the introgression showed allele-specific and chromosomal-specific pattern. In the study of introns, we found indications of mRNA mediated intron loss and non-homologous end joining (NHEJ) mediated intron gains in N. tetrasperma. We found that selection is involved in shaping intron gains and losses, and associated with intron position, intron phase and GC content. In the study of chromosomal structural rearrangements, we found a lineage specific chromosomal inversion pattern in N. tetrasperma, which indicates that inversions are unlikely to associate with the origin of the suppressed recombination and the mating system transition in N. tetrasperma. The result suggests inversions are the consequences, rather than the causes, of suppressed recombination on the mating-type chromosome of N. tetrasperma. In the final study, analyses of codon usage indicated that the region of suppressed recombination in N. tetrasperma is subjected to genomic degeneration, and selection efficiency has been much reduced in this region.

  • 1575.
    Sun, Yu
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Corcoran, Pádraic
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Åslin, Matilda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Lao, Zhiqin
    Beijing Genomic Institute.
    Li, Li
    Beijing Genomic Institute.
    Wang, Weilin
    Beijing Genomic Institute.
    Andersson, Siv
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Johannesson, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Lineage-specific chromosomal inversions in Neurospora tetraspermaManuskript (preprint) (Annet vitenskapelig)
  • 1576.
    Sun, Yu
    et al.
    South China Agr Univ, Coll Life Sci, Guangdong Prov Key Lab Prot Funct & Regulat Agr O, Guangzhou 510642, Guangdong, Peoples R China..
    Svedberg, Jesper
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Hiltunen, Markus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Corcoran, Padraic
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    Johannesson, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma2017Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, artikkel-id 1140Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A common feature of eukaryote genomes is large chromosomal regions where recombination is absent or strongly reduced, but the factors that cause this reduction are not well understood. Genomic rearrangements have often been implicated, but they may also be a consequence of recombination suppression rather than a cause. In this study, we generate eight high-quality genomic data sets of the filamentous ascomycete Neurospora tetrasperma, a fungus that lacks recombination over most of its largest chromosome. The genomes surprisingly reveal collinearity of the non-recombining regions and although large inversions are enriched in these regions, we conclude these inversions to be derived and not the cause of the suppression. To our knowledge, this is the first time that non-recombining, genic regions as large as 86% of a full chromosome (or 8 Mbp), are shown to be collinear. These findings are of significant interest for our understanding of the evolution of sex chromosomes and other supergene complexes.

  • 1577. Sun, Yu
    et al.
    Svedberg, Jesper
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Hiltunen, Markus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Corcoran, Pádraic
    Johannesson, Hanna
    Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma2017Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A common feature of eukaryote genomes is large chromosomal regions where recombination is absent or strongly reduced, but the factors that cause this reduction are not well understood. Genomic rearrangements have often been implicated, but they may also be a consequence of recombination suppression rather than a cause. In this study, we generate eight high-quality genomic datasets of N. tetrasperma, a fungus that lacks recombination over most of its largest chromosome. The genomes surprisingly reveal collinearity of the non-recombining regions and although large inversions are enriched in these regions, we conclude these inversions to be derived and not the cause of the suppression. To our knowledge, this is the first time that non-recombining, genic regions as large as 86% of a full chromosome (or 8 Mbp), are shown to be collinear. These findings are of significant interest for our understanding of the evolution of sex chromosomes and other supergene complexes.

  • 1578.
    Sun, Yu
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Tamarit, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Andersson, Siv
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites2017Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, nr 10, s. 2560-2579Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The major codon preference model suggests that codons read by tRNAs in high concentrations are preferentially utilized in highly expressed genes. However, the identity of the optimal codons differs between species although the forces driving such changes are poorly understood. We suggest that these questions can be tackled by placing codon usage studies in a phylogenetic framework and that bacterial genomes with extreme nucleotide composition biases provide informative model systems. Switches in the background substitution biases from GC to AT have occurred in Gardnerella vaginalis (GC = 32%), and from AT to GC in Lactobacillus delbrueckii (GC=62%) and Lactobacillus fermentum (GC = 63%). We show that despite the large effects on codon usage patterns by these switches, all three species evolve under selection on synonymous sites. In G. vaginalis, the dramatic codon frequency changes coincide with shifts of optimal codons. In contrast, the optimal codons have not shifted in the two Lactobacillus genomes despite an increased fraction of GC-ending codons. We suggest that all three species are in different phases of an on-going shift of optimal codons, and attribute the difference to a stronger background substitution bias and/or longer time since the switch in G. vaginalis. We show that comparative and correlative methods for optimal codon identification yield conflicting results for genomes in flux and discuss possible reasons for the mispredictions. We conclude that switches in the direction of the background substitution biases can drive major shifts in codon preference patterns even under sustained selection on synonymous codon sites.

  • 1579.
    Sun, Yu
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Whittle, Carrie-Ann
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Corcoran, Pádraic
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Johannesson, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Intron Evolution in Neurospora: the role of mutational bias and selection2015Inngår i: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 25, nr 1, s. 100-110Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We used comparative and population genomics to study intron evolutionary dynamics in the fungal model genus Neurospora. For our investigation, we used well-annotated genomes of N. crassa, N. discreta, and N. tetrasperma, and 92 resequenced genomes of N. tetrasperma from natural populations. By analyzing the four well-annotated genomes, we identified 9495 intron sites in 7619 orthologous genes. Our data supports nonhomologous end joining (NHEJ) and tandem duplication as mechanisms for intron gains in the genus and the RT-mRNA process as a mechanism for intron loss. We found a moderate intron gain rate (5.78-6.89x10(-13) intron gains per nucleotide site per year) and a high intron loss rate (7.53-13.76x10(-10) intron losses per intron sites per year) as compared to other eukaryotes. The derived intron gains and losses are skewed to high frequencies, relative to neutral SNPs, in natural populations of N. tetrasperma, suggesting that selection is involved in maintaining a high intron turnover. Furthermore, our analyses of the association between intron population-level frequency and genomic features suggest that selection is involved in shaping a 5' intron position bias and a low intron GC content. However, intron sequence analyses suggest that the gained introns were not exposed to recent selective sweeps. Taken together, this work contributes to our understanding of the importance of mutational bias and selection in shaping the intron distribution in eukaryotic genomes.

  • 1580.
    Sundberg, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Contributions to the understanding of diversity and evolution in the genus Coreomyces2018Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The Laboulbeniales is an order of enigmatic ascomycete fungi that are obligate microscopic parasites of arthropods, which are usually non-detrimental. They typically display a high degree of host specificity, and the genus Coreomyces, which is the recurring theme of this thesis, is no exception. Coreomyces is a small aquatic genus parasitising water boatmen (Corixidae). Members in this genus present something that is unique for Laboulbeniales, position specificity. This means that a parasite is restricted to a specific position on the host. This thesis aims at elucidating the patterns of host and position specificity present in the genus Coreomyces by the use of molecular markers. A second aim is to describe new taxa encountered during the course of the project. Finally we wanted to reveal what mating system is present in a member of the Laboulbeniales, something that has never been done before. Understanding the mode of sexual reproduction and to get insights into mating type organisation can give important clues to how the species patterns we observe may have evolved. To achieve these goals we first had to develop a robust and simple molecular methodology that made use of as little material as possible, preferably a single thallus. Our results showed that position specificity indeed exists in this genus, but that it is not as strict as previously presumed, all species we analysed occupied more than one position. Further we were able to show that thalli found in the same position on different hosts constitute the same species, and also that two sister species utilise the same position. We conclude that, in most cases, growth position is more important than host species or host sex in species delimitation. We confirmed the presence of four discrete taxa, two of which were described as new species, Coreomyces confusus H. Sundb. et al. and C. dextrorsus H. Sundb. et al. Finally we were able to show that C. macropus and C. confusus are likely to display a homothallic breeding system.

  • 1581.
    Sundberg, Henrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Kruys, Åsa
    Uppsala universitet, Enheten för musik och museer, Evolutionsmuseet.
    Bergsten, Johannes
    Naturhistoriska riksmuseet.
    Ekman, Stefan
    Uppsala universitet, Enheten för musik och museer, Evolutionsmuseet.
    Mating types in the genus CoreomycesManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The aim of this study was to uncover the mating system in members of the monoecious genus Coremyces (Laboulbeniales, Ascomycota). We retrieved genome sequences from five individuals using NGS methods and looked for mating type genes as well as flanking genes. The genomes represent two species, Coreomyces macropus Thaxt. (four genomes) and C. confusus H. Sundb. et al. (one genome). Our results indicate that the two species of Coreomyces are homothallic. We found both MAT1-1 and MAT1-2 in long scaffolds with high sequencing depth in four out of five genomes (MAT1-2 was not encountered in one of the genomes). The flanking SLA2 gene was observed in all five genomes, whereas APN2 was encountered only in two genomes of C. macropus. Homothallism, combined with the earlier observations that archegonia and antheridia appear in close physical proximity and that spermatia generally disperse only over very short distances, suggest that intrahaploid mating may be the norm in Coreomyces and confers an evolutionary advantage.

  • 1582.
    Sundberg, Henrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Kruys, Åsa
    Uppsala universitet, Enheten för musik och museer, Evolutionsmuseet.
    Bergsten, Johannes
    Naturhistoriska riksmuseet, Stockholm, Sweden.
    Ekman, Stefan
    Uppsala universitet, Enheten för musik och museer, Evolutionsmuseet.
    Position specificity in the genus Coreomyces (Laboulbeniomycetes, Ascomycota)2018Inngår i: Fungal Systematics and Evolution, ISSN 2589-3823, Vol. 1, nr 1, s. 217-228Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To study position specificity in the insect-parasitic fungal genus Coreomyces (Laboulbeniaceae, Laboulbeniales), we sampled corixid hosts (Corixidae, Heteroptera) in southern Scandinavia. We detected Coreomyces thalli in five different positions on the hosts. Thalli from the various positions grouped in four distinct clusters in the resulting gene trees, distinctly so in the ITS and LSU of the nuclear ribosomal DNA, less so in the SSU of the nuclear ribosomal DNA and the mitochondrial ribosomal DNA. Thalli from the left side of abdomen grouped in a single cluster, and so did thalli from the ventral right side. Thalli in the mid-ventral position turned out to be a mix of three clades, while thalli growing dorsally grouped with thalli from the left and right abdominal clades. The mid-ventral and dorsal positions were found in male hosts only. The position on the left hemelytron was shared by members from two sister clades. Statistical analyses demonstrate a significant positive correlation between clade and position on the host, but also a weak correlation between host sex and clade membership. These results indicate that sex-of-host specificity may be a non-existent extreme in a continuum, where instead weak preferences for one host sex may turn out to be frequent.

  • 1583. Sundberg, Henrik
    et al.
    Kruys, Åsa
    Bergsten, Johannes
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Ekman, Stefan
    Position specificity in the genus Coreomyces (Laboulbeniomycetes, Ascomycota)2018Inngår i: Fungal Systematics and Evolution, ISSN 2589-3823, Vol. 1, s. 217-228Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To study position specificity in the insect-parasitic fungal genus Coreomyces (Laboulbeniaceae, Laboulbeniales),

    we sampled corixid hosts (Corixidae, Heteroptera) in southern Scandinavia. We detected Coreomyces thalli in five different

    positions on the hosts. Thalli from the various positions grouped in four distinct clusters in the resulting gene trees, distinctly

    so in the ITS and LSU of the nuclear ribosomal DNA, less so in the SSU of the nuclear ribosomal DNA and the mitochondrial

    ribosomal DNA. Thalli from the left side of abdomen grouped in a single cluster, and so did thalli from the ventral right side.

    Thalli in the mid-ventral position turned out to be a mix of three clades, while thalli growing dorsally grouped with thalli from

    the left and right abdominal clades. The mid-ventral and dorsal positions were found in male hosts only. The position on the left

    hemelytron was shared by members from two sister clades. Statistical analyses demonstrate a significant positive correlation

    between clade and position on the host, but also a weak correlation between host sex and clade membership. These results

    indicate that sex-of-host specificity may be a non-existent extreme in a continuum, where instead weak preferences for one

    host sex may turn out to be frequent.

  • 1584.
    Sunde, Johanna
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Forsman, Anders
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Mate choice is not consistent with short-term effects of intraspecific admixture in the common rough woodlouse (Porcellio scaber)2016Inngår i: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 119, nr 2, s. 359-369Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Theory posits that individuals should exhibit mate preferences in part based on genetic relatedness such that fitness is maximized. Intraspecific genetic admixture can have different effects depending on the genetic characteristics and evolutionary history of the individuals and populations involved. We investigated whether female mate choice behavior in the common rough woodlouse (Porcellio scaber) matched the fitness consequences of genetic admixture. We found that most females from two populations that were in sequence introduced to one male from each population mated with both males, and further that monandrous females (females that only mated with one male) predominantly mated with males from their own population. To test for effects of genetic admixture, females from four populations were divided into two replicate pairs and assigned to mate either with a male from the same population as the female (pure) or with a male from the other population (admixed). The effect of mating treatment on the proportion of females that produced eggs and hatched young, as well as on the number and viability of offspring depended on female source population. Mating treatment had opposing effects in two of the populations, whereas there were no detectable effects in the other two populations. Contrary to what was expected, the mating patterns did not match the observed effects of genetic admixture. We discuss alternative adaptive and non-adaptive explanations for the observed patterns.

  • 1585.
    Sunde, Johanna
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Tibblin, Petter
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Larsson, Per
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Forsman, Anders
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Sex-specific effects of outbreeding on offspring quality in pike (Esox lucius)2018Inngår i: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, nr 21, s. 10448-10459Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Intraspecific genetic admixture occurs when previously separated populations withina species start interbreeding, and it can have either positive, negative, or neutral effectson reproductive performance. As there currently is no reliable predictor for theoutcome of admixture, an increased knowledge about admixture effects in differentspecies and populations is important to increase the understanding about what determinesthe response to admixture. We tested for effects of admixture on F1 offspringquality in three subpopulations of pike (Esox lucius). Gametes were collected inthe field, and eggs from each female were experimentally fertilized with milt from amale from each population (one “pure” and two “admixed” treatments). Three offspringquality measures (hatching success, fry survival, and fry length) were determinedand compared between (a) pure and admixed population combinations and (b)the sex-specifictreatments within each admixed population combination (based onthe origin of the male and female, respectively). The results suggested that althoughthere were no overall effects of admixture on offspring quality, the consequences fora given population combination could be sex-specificand thus differ depending onwhich of the parents originated from one or the other population. All offspring qualitytraits were influenced by both maternal ID and paternal ID. Sex-andindividual-specificeffects can have implications for dispersal behavior and gene flow betweennatural populations, and are important to consider in conservation efforts.

  • 1586.
    Sundman, Ann-Sofie
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Johnsson, Martin
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Jensen, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Similar recent selection criteria associated with different behavioural effects in two dog breeds2016Inngår i: Genes, Brain and Behavior, ISSN 1601-1848, E-ISSN 1601-183X, Vol. 15, nr 8, s. 750-756Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Selection during the last decades has split some established dog breeds into morphologically and behaviourally divergent types. These breed splits are interesting models for behaviour genetics since selection has often been for few and well-defined behavioural traits. The aim of this study was to explore behavioural differences between selection lines in golden and Labrador retriever, in both of which a split between a common type (pet and conformation) and a field type (hunting) has occurred. We hypothesized that the behavioural profiles of the types would be similar in both breeds. Pedigree data and results from a standardized behavioural test from 902 goldens (698 common and 204 field) and 1672 Labradors (1023 and 649) were analysed. Principal component analysis revealed six behavioural components: curiosity, play interest, chase proneness, social curiosity, social greeting and threat display. Breed and type affected all components, but interestingly there was an interaction between breed and type for most components. For example, in Labradors the common type had higher curiosity than the field type (F1,1668 = 18.359; P < 0.001), while the opposite was found in goldens (F1,897 = 65.201; P < 0.001). Heritability estimates showed considerable genetic contributions to the behavioural variations in both breeds, but different heritabilities between the types within breeds was also found, suggesting different selection pressures. In conclusion, in spite of similar genetic origin and similar recent selection criteria, types behave differently in the breeds. This suggests that the genetic architecture related to behaviour differs between the breeds.

  • 1587.
    Supraha, Luka
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Paleobiologi.
    Phenotypic variation and adaptive strategies in calcifying marine phytoplankton (Coccolithophores)2015Licentiatavhandling, med artikler (Annet vitenskapelig)
  • 1588.
    Supraha, Luka
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Paleobiologi.
    Ljubesic, Zrinka
    Univ Zagreb, Fac Sci, Dept Biol, Rooseveltov Trg 6, Zagreb 10000, Croatia.
    Henderiks, Jorijntje
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Paleobiologi. Univ Oslo, Dept Biosci, CEES, POB 1066, N-0316 Oslo, Norway.
    Combination coccospheres from the Eastern Adriatic coast: New, verified and possible life-cycle associations2018Inngår i: Marine Micropaleontology, ISSN 0377-8398, E-ISSN 1872-6186, Vol. 141, s. 23-30Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Coccolithophore life cycles involve the alternation between morphologically distinct life-cycle phases. This often leads to taxonomic issues where the life-cycle phases of the same species are described as distinct taxa. This issue can be resolved by the observation of combination coccospheres, i.e. cells bearing the coccoliths of both life-cycle phases. This study presents new observations on combination coccospheres from the highly diverse and ecologically important coccolithophore order Syracosphaerales and the genus Alisphaera. New life-cycle associations are revealed between Syracosphaera hirsuta and Corisphaera strigilis, and between Alisphaera unicornis and a nannolith-producing Polycrater galapagensis. The life-cycle association of Syracosphaera marginiporata Anthosphaera sp. type B is verified. A possible association between Rhabdosphaera xiphos and an unidentified holococcolith-bearing morphotype is proposed and needs to be verified in future investigations. The appropriate taxonomic revisions are conducted following the taxonomic principle of priority and recommended practices for naming the coccolithophore life-cycle phases.

  • 1589. Sutherland, William J.
    et al.
    Aveling, Rosalind
    Brooks, Thomas M.
    Clout, Mick
    Dicks, Lynn V.
    Fellman, Liz
    Fleishman, Erica
    Gibbons, David W.
    Keim, Brandon
    Lickorish, Fiona
    Monk, Kathryn A.
    Mortimer, Diana
    Peck, Lloyd S.
    Pretty, Jules
    Rockström, Johan
    Stockholms universitet, Naturvetenskapliga fakulteten, Stockholm Resilience Centre.
    Rodriguez, Jon Paul
    Smith, Rebecca K.
    Spalding, Mark D.
    Tonneijck, Femke H.
    Watkinson, Andrew R.
    A horizon scan of global conservation issues for 20142014Inngår i: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 29, nr 1, s. 15-22Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    This paper presents the output of our fifth annual horizon-scanning exercise, which aims to identify topics that increasingly may affect conservation of biological diversity, but have yet to be widely considered. A team of professional horizon scanners, researchers, practitioners, and a journalist identified 15 topics which were identified via an iterative, Delphi-like process. The 15 topics include a carbon market induced financial crash, rapid geographic expansion of macroalgal cultivation, genetic control of invasive species, probiotic therapy for amphibians, and an emerging snake fungal disease.

  • 1590.
    Svanbäck, Richard
    et al.
    Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
    Schluter, Dolph
    Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
    Niche Specialization Influences Adaptive Phenotypic Plasticity in the Threespine Stickleback2012Inngår i: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 180, nr 1, s. 50-59Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phenotypic plasticity may be favored in generalist populations if it increases niche width, even in temporally constant environments. Phenotypic plasticity can increase the frequency of extreme phenotypes in a population and thus allow it to make use of a wide resource spectrum. Here we test the prediction that generalist populations should be more plastic than specialists. In a common-garden experiment, we show that solitary, generalist populations of threespine sticklebacks inhabiting small coastal lakes of British Columbia have a higher degree of morphological plasticity than the more specialized sympatric limnetic and benthic species. The ancestral marine stickleback showed low levels of plasticity similar to those of sympatric sticklebacks, implying that the greater plasticity of the generalist population has evolved recently. Measurements of wild populations show that those with mean trait values intermediate between the benthic and limnetic values indeed have higher morphological variation. Our data indicate that plasticity can evolve rapidly after colonization of a new environment in response to changing niche use.

  • 1591.
    Svedberg, Jesper
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Catching the Spore killers: Genomic conflict and genome evolution in Neurospora2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    A genome is shaped by many different forces. Recombination can for instance both create and maintain genetic diversity, but the need to locally reduce recombination rates will also leave specific signatures. Genetic elements can act selfishly and spreading at the expense of the rest of the genome can leave marks of their activity, as can mechanisms that suppresses them, in a phenomenon known as genomic conflict. In this thesis, I have studied the forces driving genome evolution, using modern genome sequencing techniques and with a special focus on a class of selfish genetic elements known as Spore killers found in the fungus Neurospora. First, we show novel findings on large-scale suppression of recombination by non-structural means in the N. tetrasperma genomes. In contrary, in the genomic region harbouring the spore killer elements Sk-2 and Sk-3 of N. intermedia, a dense set of inversions that are interspersed with transposable elements have accumulated. The inversions are unique for each killer type, showing that they have a long separated evolutionary history and likely have established themselves independently. For the Sk-2 haplotype, where we have polymorphism data, we see signs of relaxed selection, which is consistent with the hypothesis that recombination suppression reduces the efficacy of selection in this region. These results show the strong effects the divergent selective forces of genomic conflicts can have on chromosome architecture. Furthermore, we investigate the hypothesis that spore killing can drive reproductive isolation, by comparing the fertility of crosses between N. metzenbergii and either killer or non-killer N. intermedia strains. We show that crosses with spore killer strains have lower fertility, which cannot be explained by the killing itself, but is potentially caused by an incompatibility gene captured in the non-recombining region. Finally, we identified the genetic element responsible for causing spore killing in the Sk-1 spore killer strains found in N. sitophila. Unlike the Sk-2 and Sk-3 elements, Sk-1 is not connected to a large, non-recombining region, but is caused by a single locus, and we also find indications that this locus was introgressed from N. hispaniola.

  • 1592.
    Svedberg, Jesper
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Hosseini, Sara
    Chen, Jun
    Mozgova, Iva
    Hennig, Lars
    Manitchotpisit, Pennapa
    Hammond, Thomas M.
    Lascoux, Martin
    Johannesson, Hanna
    The effect of genomic conflict on genome evolution in Neurospora intermediaManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Genomic conflicts are predicted to have a major influence on genome evolution, but empirical data is needed in order to confirm or refute this prediction. In this study, we used a genomic approach to address the influence of genomic conflicts, caused by selfish genetic elements, on genome evolution in the model fungus Neurospora intermedia. We gathered high-quality genomic data from sixteen strains of Neurospora by using the PacBio RSII long-read sequencing platform. Six of these strains carry the meiotic drive element Sk-2 or Sk-3, which are multigene systems of killer and resistance loci linked together in haplotypes. We show that in the N. intermedia genomes, in which an array of protective mechanisms act to limit the negative effects of selfish DNA, both the Sk-2 and Sk-3 haplotypes have accumulated a dense set of inversions that are interspersed with transposable elements. The inversions are unique for each killer type, showing that they have a long separated evolutionary history and likely have established themselves as meiotic drivers independently. For the Sk-2 haplotype, for which we have polymorphism-data, we see signs of relaxed selection, which is consistent with the hypothesis that recombination suppression reduces the efficacy of selection in this region. Thus, our data indicates that albeit N. intermedia possesses an active genome defence system, selfish genetic elements have worked in concert and significantly affected the evolutionary trajectory of chromosome 3 in this species.

  • 1593.
    Svedberg, Jesper
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Hosseini, Sara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Chen, Jun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Vogan, Aaron A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Mozgova, Iva
    Swedish Univ Agr Sci, Dept Plant Biol, POB 7080, SE-75007 Uppsala, Sweden;Swedish Univ Agr Sci, Linnean Ctr Plant Biol, POB 7080, SE-75007 Uppsala, Sweden;Czech Acad Sci, Inst Microbiol, Ctr Algatech, CZ-37981 Trebon, Czech Republic.
    Hennig, Lars
    Swedish Univ Agr Sci, Dept Plant Biol, POB 7080, SE-75007 Uppsala, Sweden;Swedish Univ Agr Sci, Linnean Ctr Plant Biol, POB 7080, SE-75007 Uppsala, Sweden.
    Manitchotpisit, Pennapa
    Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA.
    Abusharekh, Anna
    Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA.
    Hammond, Thomas M.
    Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Johannesson, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements2018Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, artikkel-id 4242Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.

  • 1594.
    Svedberg, Jesper
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Vogan, Aaron
    Rhoades, Nicholas A.
    Sarmarajeewa, Dilini
    Hammond, Thomas M.
    Lascoux, Martin
    Johannesson, Hanna
    A single gene causes meiotic drive in Neurospora sitophilaManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Meiotic drive in Neurospora was first identified in Neurospora sitophila over forty years ago. Since drive in this fungus results in “spore killing”, the drive was designated Sk-1. The locus responsible for killing has until now been unknown. Here we sequenced 56 N. sitophila strains from natural populations, using paired-end sequencing on the Illumina HiSeq platform, and used this population genomic data to identify a locus on chromosome VI that significantly associates with the killing phenotypewe have used Illumina technology to generate whole genome sequence data for 56 wild N. sitophila strains. Using a genome wide association test we have identified the locus responsible for the Sk-1 phenotype on chromosome VI. We call the locus nkl1. By using the PacBio RSII platform, we generated high quality genome assemblies of four N. sitophila strains (two Sk-1 killers and two sensitives) and verified that no structural rearrangements were found in this region or on other chromosomes. We verified by laboratory crosses that the allelic variants of nkl1 show segregation distortion, and generated deletion mutants to demonstrate that the locus is responsible both for killing and resistance. We show demonstrate that the element is likely to have been introgressed from the closely related species, N. hispaniola. We identified three subclades in N. sitophila is split up into three subclades, in one of which Sk-1 is fixed for Sk-1, one another where Sk-1 is absent, and a third where killers and sensitives appear to intermix. This indicates that Sk-1 is currently invading N. sitophila through matings between diverged lineages.

  • 1595.
    Svennungsen, Thomas Owens
    et al.
    Univeristy of Oslo, Norway.
    Holen, Öistein Haugsten
    Univeristy of Oslo, Norway.
    Leimar, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Inducible Defenses: Continuous Reaction Norms or Threshold Traits?2011Inngår i: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 178, nr 3, s. 397-410Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phenotypically plastic traits can be expressed as continuous reaction norms or as threshold traits, but little is known about the selective conditions that favor one over the other. We study this question using a model of prey defenses in which prey can induce any level of defense conditional on cues that are informative of local predator density. The model incorporates a trade-off between defense expression and fecundity and feedback between the defense level of prey and predator attack rates. Both continuous reaction norms and threshold traits can emerge as evolutionarily stable solutions of defense induction, and we show that the shape of the trade-off curve plays a key role in determining the outcome. Threshold traits are favored when selection is disruptive. Ecological conditions that favor defense dimorphisms in the absence of cues will favor threshold traits in the presence of slightly informative cues. We caution that continuous reaction norms and threshold traits may result in similar patterns of defense expression at the population level, and we discuss potential pitfalls of inferring reaction norm type from observational data.

  • 1596.
    Svensson, Erik I.
    et al.
    Lund Univ, Dept Biol, S-22362 Lund, Sweden.
    Goedert, Debora
    Dartmouth Coll, Dept Biol Sci, Hanover, NH 03755 USA.
    Gomez-Llano, Miguel A.
    Lund Univ, Dept Biol, S-22362 Lund, Sweden.
    Spagopoulou, Foteini
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Nava-Bolanos, Angela
    Univ Nacl Autonoma Mexico, Inst Ecol, Dept Ecol Evolut, Apdo Postal 70-275,Ciudad Univ, Mexico City 04510, DF, Mexico;Univ Nacl Autonoma Mexico, Fac Ciencias, Secret Educ Abierta & Continua, CU, Ave Univ 3000, Mexico City 04510, DF, Mexico.
    Booksmythe, Isobel
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia.
    Sex differences in local adaptation: what can we learn from reciprocal transplant experiments?2018Inngår i: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 373, nr 1757, artikkel-id 20170420Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Local adaptation is of fundamental interest to evolutionary biologists. Traditionally, local adaptation has been studied using reciprocal transplant experiments to quantify fitness differences between residents and immigrants in pairwise transplants between study populations. Previous studies have detected local adaptation in some cases, but others have shown lack of adaptation or even maladaptation. Recently, the importance of different fitness components, such as survival and fecundity, to local adaptation have been emphasized. Here, we address another neglected aspect in studies of local adaptation: sex differences. Given the ubiquity of sexual dimorphism in life histories and phenotypic traits, this neglect is surprising, but may be partly explained by differences in research traditions and terminology in the fields of local adaptation and sexual selection. Studies that investigate differences in mating success between resident and immigrants across populations tend to be framed in terms of reproductive and behavioural isolation, rather than local adaptation. We briefly review the published literature that bridges these areas and suggest that reciprocal transplant experiments could benefit from quantifying both male and female fitness components. Such a more integrative research approach could clarify the role of sex differences in the evolution of local adaptations. 

  • 1597.
    Svensson, P. Andreas
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    A new goby research lab in the central Baltic Proper2013Konferansepaper (Annet vitenskapelig)
  • 1598.
    Svensson, P. Andreas
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Adaptations and strategies for paternal care in a desert-dwelling fish. 2009Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Parental care enhances offspring development and survival, but also imposes costs to the caring parent by reducing, for example, future reproduction. This is especially true in species with paternal care, that is, where the male cares for the offspring. Both anatomical and behavioural adaptations are expected to have evolved in order to economize paternal care. The Australian desert goby is a sexually dimorphic species that expresses exclusive paternal care. Males have larger pectoral fins relative to females, possibly to assist in the fanning of the eggs. Males also strategically adjust their parental effort to maximise their fitness. In laboratory experiments, we found that males with larger fins fanned at a lower frequency. The presence of ready-to-spawn females led to a reduction in paternal care effort suggesting a temporal trade-off between care of existing eggs and courtship of additional females. In addition, both the degree and type of filial cannibalism was related to the size of the clutch, and, therefore, female quality. Our results suggest that desert gobies have evolved both morphological adaptations and behavioural strategies to balance the costs and benefits of paternal care.

  • 1599.
    Svensson, P. Andreas
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Female coloration and beneficial egg carotenoids2006Konferansepaper (Fagfellevurdert)
  • 1600.
    Svensson, P. Andreas
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Female coloration and beneficial egg carotenoids2007Konferansepaper (Annet vitenskapelig)
29303132333435 1551 - 1600 of 1859
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