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  • 1.
    Abalde, Samuel
    et al.
    Swedish Museum Nat Hist, Dept Zool, Stockholm, Sweden..
    Tellgren-Roth, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Heintz, Julia
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Vinnere Pettersson, Olga
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jondelius, Ulf
    Swedish Museum Nat Hist, Dept Zool, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden..
    The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes2023In: Frontiers in Genetics, E-ISSN 1664-8021, Vol. 14, article id 1244493Article in journal (Refereed)
    Abstract [en]

    Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group’s main clades and whose origin has been dated more than 400 million years ago.

    Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades.

    Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system.

    Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.

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  • 2.
    Abalo, Xesus
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Boije: Zebrafish Neuronal Networks. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical diabetology and metabolism.
    Lagman, David
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. Univ Bergen, Sars Int Ctr Marine Mol Biol, Bergen, Norway.
    Heras, Gabriel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. Uppsala University, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Dept Physiol & Pharmacol, Stockholm, Sweden.
    del Pozo, Ana
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Boije: Zebrafish Neuronal Networks. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Eggert, Joel
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. Emory Univ, Dept Med, Atlanta, GA 30322 USA.
    Larhammar, Dan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Larhammar: Pharmacology.
    Circadian regulation of phosphodiesterase 6 genes in zebrafish differs between cones and rods: Implications for photopic and scotopic vision2020In: Vision Research, ISSN 0042-6989, E-ISSN 1878-5646, Vol. 166, p. 43-51Article in journal (Refereed)
    Abstract [en]

    A correlation is known to exist between visual sensitivity and oscillations in red opsin and rhodopsin gene expression in zebrafish, both regulated by the clock gene. This indicates that an endogenous circadian clock regulates behavioural visual sensitivity, apart from the regulation exerted by the pineal organ. However, the specific mechanisms for cones (photopic vision) and rods (scotopic vision) are poorly understood. In this work, we performed gene expression, cosinor and immunohistochemical analyses to investigate other key genes involved in light perception, encoding the different subunits of phosphodiesterase pde6 and transducin G alpha(T), in constant lighting conditions and compared to normal light-dark conditions. We found that cones display prominent circadian oscillations in mRNA levels for the inhibitory subunit gene pde6ha that could contribute to the regulation of photopic sensitivity by preventing overstimulation in photopic conditions. In rods, the mRNA levels of the inhibitory subunit gene pde6ga oscillate under normal conditions and dampen down in constant light but continue oscillating in constant darkness. There is an increase in total relative expression for pde6gb in constant conditions. These observations, together with previous data, suggest a complex regulation of the scotopic sensitivity involving endogenous and non-endogenous components, possibly present also in other teleost species. The G alpha(T) genes do not display mRNA oscillations and therefore may not be essential for the circadian regulation of photosensitivity. In summary, our results support different regulation for the zebrafish photopic and scotopic sensitivities and suggest circadian regulation of pde6ha as a key factor regulating photopic sensitivity, while the regulatory mechanisms in rods appear to be more complex.

  • 3.
    Abdalaal, Hind
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala.
    Deciphering molecular mechanisms in the evolution of new functions2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The evolution of new genes and functions is considered to be a major contributor to biological diversity in organisms. Through de novo origination, “duplication and divergence”, and horizontal gene transfer, organisms can acquire new genetic material that can evolve to perform novel functions. In this thesis, we investigate how functional trade-offs, “gene duplication and amplification”, and neutral divergence contribute to the emergence of a new function from a preexisting gene.

     In Paper i, we investigated the ability of Salmonella enterica to compensate for the loss of peptide release factor 1 (RFI) and the potential of peptide release factor 2 (RF2) to gain a new function to replace RFI. The amplification of RF2 and accumulated mutations within RF2 were the main evolutionary routes by which the fitness cost was restored. However, further characterization of the evolved RF2 showed a toxic effect to the cell due to the termination on tryptophan codon (UGG). This evolutionary trade-off - which we named “collateral toxicity” - might present a serious barrier for evolving an efficient RF2 to replace RF1.

    In Paper ii, we determined whether we could evolve a generalist enzyme with two functions (HisA + TrpF) from the specialist enzyme HisA, which can only synthesize histidine. In a previous study, we showed that HisA evolved a TrpF activity through strong trade-off trajectories. Here, we developed a selection scheme in which we constantly selected for keeping the original function (HisA), while intermittently selecting for the new function (TrpF). Our results showed that all evolved lineages shared the same “stepping stone” mutations in the hisA gene, which enabled them to grow well in the absence of both histidine and tryptophan. Additional accumulated mutations in the hisA gene gave the strains an increased ability to grow without both amino acids, indicating that the HisA enzyme evolved to be an efficient generalist.  

    In Paper iii, we explored how differences between diverged orthologs influence evolvability. We generated artificial orthologs using a random mutagenesis approach. First, we screened for orthologs with a lower HisA activity and then selected for orthologs with a higher HisA activity; these steps were repeated in alternating rounds. We then tested the ability of each ortholog to evolve  TrpF activity. As expected, the orthologs showed varying abilities to evolve the new function. In particular, orthologs with higher HisA activity levels showed both a higher potential to evolve the new function and a higher TrpF activity when they acquired the new function. 

    List of papers
    1. Collateral toxicity limits the evolution of bacterial Release Factor 2 towards total omnipotence
    Open this publication in new window or tab >>Collateral toxicity limits the evolution of bacterial Release Factor 2 towards total omnipotence
    Show others...
    2020 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, no 10, p. 2918-2930Article in journal (Refereed) Published
    Abstract [en]

    When new genes evolve through modification of existing genes, there are often trade-offs between the new and original functions, making gene duplication and amplification necessary to buffer deleterious effects on the original function. We have used experimental evolution of a bacterial strain lacking peptide release factor 1 (RF1) in order to study how peptide release factor 2 (RF2) evolves to compensate the loss of RF1. As expected, amplification of the RF2-encoding gene prfB to high copy number was a rapid initial response, followed by the appearance of mutations in RF2 and other components of the translation machinery. Characterization of the evolved RF2 variants by their effects on bacterial growth rate, reporter gene expression, and in vitro translation termination reveals a complex picture of reduced discrimination between the cognate and near cognate stop codons and highlight a functional trade-off that we term “collateral toxicity”. We suggest that this type of trade-off may be a more serious obstacle in new gene evolution than the more commonly discussed evolutionary trade-offs between “old” and “new” functions of a gene, as it cannot be overcome by gene copy number changes. Further, we suggest a model for how RF2 autoregulation responds not only to alterations in the demand for RF2 activity, but also for RF1 activity.

    Place, publisher, year, edition, pages
    Oxford University Press (OUP), 2020
    National Category
    Evolutionary Biology Microbiology Biochemistry and Molecular Biology
    Research subject
    Biology with specialization in Molecular Evolution
    Identifiers
    urn:nbn:se:uu:diva-410852 (URN)10.1093/molbev/msaa129 (DOI)000593115800011 ()32437534 (PubMedID)
    Note

    The two first authors contributed equally to this work.

    Available from: 2020-05-22 Created: 2020-05-22 Last updated: 2023-06-21Bibliographically approved
    2. Intermittent selection directs evolution of a specialist enzyme to become a generalist
    Open this publication in new window or tab >>Intermittent selection directs evolution of a specialist enzyme to become a generalist
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    A mutation that introduces a new enzymatic function can be accompanied by a trade-off between the original function and the new function. We previously tested the evolutionary trajectories of Salmonella enterica HisA enzyme (catalyze the fourth step in histidine biosynthesis) towards TrpF activity (catalyze the third step in tryptophan biosynthesis). The majority of the mutations that introduced TrpF activity led to a complete loss of detectable HisA activity. In the rare hisA mutants that kept HisA activity, HisA activity was lost when selecting for mutations that improved TrpF activity. However, some natural HisA orthologs had dual (HisA and TrpF) activities, which has evolved from a specialist HisA.

    The present study was designed to investigate whether Salmonella enterica HisA can evolve into a generalist (HisA+TrpF) enzyme, despite the strong trade-off between the original function and the new function. Therefore, we allowed trpF-deleted Salmonella enterica with or without a mutator phenotype to evolve in a low concentration of tryptophan. This allowed it to grow for a few generations in relaxed selection, which was followed by several days of strong selection (tryptophan depletion). In this setup, it was never lethal to not have TrpF activity, but it would be lethal to lose HisA activity.

    These cycled lineages circumvented the tryptophan starvation by loss of function in the tryptophan biosynthesis pathway or by accumulating mutations in hisA gene. The accumulated mutations introduced bifunctionality to the hisA alleles, which was more common in the lineages with the mutator phenotype. These alleles became increasingly efficient in performing both functions when evolved further using the same conditions. Our results indicate that it is possible to evolve an efficient generalist HisA when we use a selection condition that is more likely to occur in nature (a fluctuating environment).

     

     

    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Microbiology; Biology with specialization in Molecular Evolution
    Identifiers
    urn:nbn:se:uu:diva-423324 (URN)
    Available from: 2020-10-25 Created: 2020-10-25 Last updated: 2020-10-25
    3. Evolvability of orthologous genes
    Open this publication in new window or tab >>Evolvability of orthologous genes
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The divergence of orthologous genes is usually attributed to the slow and steady accumulation of neutral or nearly neutral mutations. It is known that present-day orthologous genes have a common ancestor and still perform the same function with about the same performance. Natural orthologs differ from each other not only in sequence, but also in physical properties such as their tolerance of mutations and their potential to evolve new functions. However, we currently have a poor understanding of how mutations that accumulate during the sequence divergence of orthologous genes affect their evolvability.

    In this study, we generated a library of laboratory-evolved orthologous genes for studying how mutations and combinations of mutations (deleterious and compensatory mutations) affect evolvability. We simulated what could happen during the divergence of orthologous genes where fixation of a deleterious mutation is followed by a compensatory mutation. We have subjected one of histidine biosynthetic genes hisA from Salmonella enterica to alternating rounds of weak selection (by random mutagenesis through error-prone PCR subsequent screens for partial loss of hisA function) followed by strong purifying selection (another round of random mutagenesis and subsequent selection for restored hisA function).

    The diverging lineages were tested for their ability to evolve TrpF activity and were compared with the WT hisA using a fluctuation test. Our results confirmed that orthologous enzymes had differing abilities to evolve the new function. The HisA orthologs with restored function had evolved adaptive genotypes with higher TrpF activity. We suggest that these orthologs may have a higher stability, which is known to increase evolutionary potential by increasing the tolerance for the otherwise destabilizing mutations that confer the new function.

     

    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Microbiology
    Identifiers
    urn:nbn:se:uu:diva-423416 (URN)
    Available from: 2020-10-25 Created: 2020-10-25 Last updated: 2020-10-25
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  • 4.
    Abdalaal, Hind
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pundir, Shreya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Ge, Xueliang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Sanyal, Suparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Näsvall, Joakim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Collateral toxicity limits the evolution of bacterial Release Factor 2 towards total omnipotence2020In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, no 10, p. 2918-2930Article in journal (Refereed)
    Abstract [en]

    When new genes evolve through modification of existing genes, there are often trade-offs between the new and original functions, making gene duplication and amplification necessary to buffer deleterious effects on the original function. We have used experimental evolution of a bacterial strain lacking peptide release factor 1 (RF1) in order to study how peptide release factor 2 (RF2) evolves to compensate the loss of RF1. As expected, amplification of the RF2-encoding gene prfB to high copy number was a rapid initial response, followed by the appearance of mutations in RF2 and other components of the translation machinery. Characterization of the evolved RF2 variants by their effects on bacterial growth rate, reporter gene expression, and in vitro translation termination reveals a complex picture of reduced discrimination between the cognate and near cognate stop codons and highlight a functional trade-off that we term “collateral toxicity”. We suggest that this type of trade-off may be a more serious obstacle in new gene evolution than the more commonly discussed evolutionary trade-offs between “old” and “new” functions of a gene, as it cannot be overcome by gene copy number changes. Further, we suggest a model for how RF2 autoregulation responds not only to alterations in the demand for RF2 activity, but also for RF1 activity.

    Download full text (pdf)
    fulltext
  • 5.
    Abel, Pascal
    et al.
    Eberhani Karls Univ Tubingen, Senckenberg Ctr Human Evolut & Palaeoenvironm, Sigwartstr 28, D-72076 Tubingen, Germany..
    Hornung, Jahn
    Niedersachs Landesmuseum Hannover, Willy Brandt Allee 5, D-30169 Hannover, Germany..
    Kear, Benjamin P.
    Uppsala University, Music and Museums, Museum of Evolution.
    Sachs, Sven
    Nat Kunde Museum Bielefeld, Abt Geowissensch, Adenauerpl 2, D-33602 Bielefeld, Germany..
    An anhanguerian pterodactyloid mandible from the lower Valanginian of Northern Germany, and the German record of Cretaceous pterosaurs2021In: Acta Palaeontologica Polonica, ISSN 0567-7920, E-ISSN 1732-2421, Vol. 66, no 3, p. S5-S12Article in journal (Refereed)
    Abstract [en]

    The record of Cretaceous pterosaur remains from Germany is sparse. The material recovered to date includes the fragmentary holotypes of Targaryendraco wiedenrothi and Ctenochasma roemeri, as well as a few isolated pterodactyloid teeth and some indeterminate skeletal elements, together with a plaster cast of a large Purbeckopus manus imprint. Here, we report the discovery of a pterodactyloid pterosaur mandible from lower Valanginian strata of the Stadthagen Formation in the Lower Saxony Basin of Northern Germany. Based on the size and spacing of its alveoli, this fossil is attributable to the cosmopolitan Early Cretaceous pteranodontoid clade Anhangueria. Moreover, it represents the first and only known pterosaur from the Valanginian of Germany and is one of only a handful Valanganian pterosaur occurrences presently recognized worldwide. In addition to the approximately coeval Coloborhynchus clavirostris from the Hastings Bed Group of southern England, the Stadthagen Formation pterosaur mandible is among the stratigraphically oldest identifiable anhanguerians.

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    FULLTEXT01
  • 6.
    Adl, Sina M.
    et al.
    Univ Saskatchewan, Dept Soil Sci, Coll Agr & Bioresources, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
    Bass, David
    Nat Hist Museum, Dept Life Sci, Cromwell Rd, London SW7 5BD, England;CEFAS, Barrack Rd, Weymouth DT4 8UB, Dorset, England.
    Lane, Christopher E.
    Univ Rhode Isl, Dept Biol Sci, Kingston, RI 02881 USA.
    Lukes, Julius
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic;Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic.
    Schoch, Conrad L.
    Natl Inst Biotechnol Informat, Natl Lib Med, NIH, Bethesda, MD 20892 USA.
    Smirnov, Alexey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Agatha, Sabine
    Univ Salzburg, Dept Biosci, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Berney, Cedric
    CNRS, UMR 7144 AD2M, Grp Evolut Protistes & Ecosyst Pelag, Stn Biol Roscoff, Pl Georges Teissier, F-29680 Roscoff, France.
    Brown, Matthew W.
    Mississippi State Univ, Dept Biol Sci, Starkville, MS 39762 USA;Mississippi State Univ, Inst Genom Biocomp & Biotechnol, Starkville, MS 39762 USA.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Cepicka, Ivan
    Charles Univ Prague, Dept Zool, Fac Sci, Vinicna 7, CR-12844 Prague, Czech Republic.
    Chistyakova, Lyudmila
    St Petersburg State Univ, Core Facil Ctr Culture Collect Microorganisms, St Petersburg 198504, Russia.
    del Campo, Javier
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Dunthorn, Micah
    Univ Kaiserslautern, Dept Ecol, Erwin Schroedinger St, D-67663 Kaiserslautern, Germany;Univ Duisburg Essen, Dept Eukaryot Microbiol, Univ Str 5, D-45141 Essen, Germany.
    Edvardsen, Bente
    Univ Oslo, Dept Biosci, POB 1066 Blindern, N-0316 Oslo, Norway.
    Eglit, Yana
    Dalhousie Univ, Dept Biol, Halifax B3H 4R2, NS, Canada.
    Guillou, Laure
    Univ Paris 06, Sorbonne Univ, Paris 6, CNRS,UMR 7144 AD2M,Stn Biol Roscoff, Pl Georges Teissier,,CS90074, F-29688 Roscoff, France.
    Hampl, Vladimir
    Charles Univ Prague, Dept Parasitol, Fac Sci, BIOCEV, Prumyslov 595, Vestec 25242, Czech Republic.
    Heiss, Aaron A.
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Hoppenrath, Mona
    DZMB German Ctr Marine Biodivers Res, D-26382 Wilhelmshaven, Germany.
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Karnkowska, Anna
    Univ Warsaw, Dept Mol Phylogenet & Evolut, PL-02089 Warsaw, Poland.
    Karpov, Sergey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Kim, Eunsoo
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Kolisko, Martin
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic.
    Kudryavtsev, Alexander
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Lahr, Daniel J. G.
    Univ Sao Paulo, Dept Zool, Inst Biosci, Matao Travessa 14 Cidade Univ, BR-05508090 Sao Paulo, SP, Brazil.
    Lara, Enrique
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;CSIC, Real Jardim Bot,Plaza Murillo 2, E-28014 Madrid, Spain.
    Le Gall, Line
    Sorbonne Univ, Museum Natl Hist Nat, Inst Systemat Evolut Biodiversit, 57 Rue Cuvier,CP 39, F-75005 Paris, France.
    Lynn, Denis H.
    Univ Guelph, Dept Integrat Biol, Summerlee Sci Complex, Guelph, ON N1G 2W1, Canada;Univ British Columbia, Dept Zool, 4200-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.
    Mann, David G.
    Royal Bot Garden, Edinburgh EH3 5LR, Midlothian, Scotland;Inst Agrifood Res & Technol, C Poble Nou Km 5-5, E-43540 San Carlos de la Rapita, Spain.
    Massana, Ramon
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Mitchell, Edward A. D.
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;Jardin Bot Neuchatel,Chemin Perthuis du Salut 58, CH-2000 Neuchatel, Switzerland.
    Morrow, Christine
    Natl Museums Northern Ireland, Dept Nat Sci, 153 Bangor Rd, Holywood BT18 0EU, England.
    Park, Jong Soo
    Kyungpook Natl Univ, Sch Earth Syst Sci, Dept Oceanog, Daegu, South Korea;Kyungpook Natl Univ, Sch Earth Syst Sci, Kyungpook Inst Oceanog, Daegu, South Korea.
    Pawlowski, Jan W.
    Univ Geneva, Dept Genet & Evolut, CH-1211 Geneva 4, Switzerland.
    Powell, Martha J.
    Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA.
    Richter, Daniel J.
    Univ Pompeu Fabra, CSIC, Inst Biol Evolut, Passeig Maritim Barceloneta 37-49, Barcelona 08003, Spain.
    Rueckert, Sonja
    Edinburgh Napier Univ, Sch Appl Sci, Edinburgh EH11 4BN, Midlothian, Scotland.
    Shadwick, Lora
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Shimano, Satoshi
    Hosei Univ, Sci Res Ctr, Chiyoda Ku, 2-17-1 Fujimi, Tokyo, Japan.
    Spiegel, Frederick W.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Torruella, Guifre
    Univ Paris XI, Lab Evolut & Systemat, F-91405 Orsay, France.
    Youssef, Noha
    Oklahoma State Univ, Dept Microbiol & Mol Genet, Stillwater, OK 74074 USA.
    Zlatogursky, Vasily V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Zhang, Qianqian
    Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
    Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes2019In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 66, no 1, p. 4-119Article in journal (Refereed)
    Abstract [en]

    This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

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  • 7.
    Agic, Heda
    et al.
    Univ Calif Santa Barbara, Dept Earth Sci, Santa Barbara, CA 93106 USA..
    Hogstrom, Anette E. S.
    UiT Arctic Univ Norway, Arctic Univ Museum Norway, Tromso, Norway..
    Jensen, Soren
    Univ Extremadura, Area Paleontol, Badajoz, Spain..
    Ebbestad, Jan Ove R.
    Uppsala University, Music and Museums, Museum of Evolution.
    Vickers-Rich, Patricia
    Monash Univ, Sch Earth Atmosphere & Environm, Clayton, Vic, Australia.;Swinburne Univ Technol, Sch Sci, Dept Chem & Biotechnol, Hawthorn, Vic, Australia..
    Hall, Michael
    Monash Univ, Sch Earth Atmosphere & Environm, Clayton, Vic, Australia..
    Matthews, Jack J.
    Oxford Univ Museum Nat Hist, Oxford, England..
    Meinhold, Guido
    TU Bergakad Freiberg, Inst Geol, Freiberg, Germany.;Univ Gottingen, Dept Sedimentol & Environm Geol, Gottingen, Germany..
    Hoyberget, Magne
    Rennesveien 14, Mandal, Norway..
    Taylor, Wendy L.
    Univ Cape Town, Dept Geol Sci, Rondebosch, South Africa..
    Late Ediacaran occurrences of the organic-walled microfossils Granomarginata and flask-shaped Lagoenaforma collaris gen. et sp. nov.2022In: Geological Magazine, ISSN 0016-7568, E-ISSN 1469-5081, Vol. 159, no 7, p. 1071-1092, article id PII S0016756821001096Article in journal (Refereed)
    Abstract [en]

    New occurrences of flask-shaped and envelope-bearing microfossils, including the predominantly Cambrian taxon Granomarginata, are reported from new localities, as well as from earlier in time (Ediacaran) than previously known. The stratigraphic range of Granomarginata extends into the Cambrian System, where it had a cosmopolitan distribution. This newly reported Ediacaran record includes areas from Norway (Baltica), Newfoundland (Avalonia) and Namibia (adjacent to the Kalahari Craton), and puts the oldest global occurrence of Granomarginata in the Indreelva Member (< 563 Ma) of the Stahpogieddi Formation on the Digermulen Peninsula, Arctic Norway. Although Granomarginata is rare within the assemblage, these new occurrences together with previously reported occurrences from India and Poland, suggest a potentially widespread palaeogeographic distribution of Granomarginata through the middle-late Ediacaran interval. A new flask-shaped microfossil Lagoenaforma collaris gen. et sp. nov. is also reported in horizons containing Granomarginata from the Stahpogieddi Formation in Norway and the Dabis Formation in Namibia, and flask-shaped fossils are also found in the Gibbett Hill Formation in Newfoundland. The Granomarginata-Lagoenaforma association, in addition to a low-diversity organic-walled microfossil assemblage, occurs in the strata postdating the Shuram carbon isotope excursion, and may eventually be of use in terminal Ediacaran biostratigraphy. These older occurrences of Granomarginata add to a growing record of body fossil taxa spanning the Ediacaran-Cambrian boundary.

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  • 8.
    Agić, Heda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Univ Calif Santa Barbara, Dept Earth Sci, Santa Barbara, CA 93106 USA.
    Högström, Anette E. S.
    UiT Arctic Univ Norway, Arctic Univ Museum Norway, N-9037 Tromso, Norway.
    Moczydlowska, Malgorzata
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Jensen, Sören
    Univ Extremadura, Area Paleontol, E-06006 Badajoz, Spain.
    Palacios, Teodoro
    Univ Extremadura, Area Paleontol, E-06006 Badajoz, Spain.
    Meinhold, Guido
    Keele Univ, Sch Geog Geol & Environm, Keele ST5 5BG, Staffs, England;Univ Gottingen, Dept Sedimentol & Environm Geol, Goldschmidtstr 3, D-37077 Gottingen, Germany.
    Ebbestad, Jan Ove R.
    Uppsala University, Music and Museums, Museum of Evolution.
    Taylor, Wendy L.
    Univ Cape Town, Dept Geol Sci, ZA-7701 Rondebosch, South Africa.
    Höyberget, Magne
    Rennesveien 14, N-4513 Mandal, Norway.
    Organically-preserved multicellular eukaryote from the early Ediacaran Nyborg Formation, Arctic Norway2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 14659Article in journal (Refereed)
    Abstract [en]

    Eukaryotic multicellularity originated in the Mesoproterozoic Era and evolved multiple times since, yet early multicellular fossils are scarce until the terminal Neoproterozoic and often restricted to cases of exceptional preservation. Here we describe unusual organically-preserved fossils from mudrocks, that provide support for the presence of organisms with differentiated cells (potentially an epithelial layer) in the late Neoproterozoic. Cyathinema digermulense gen. et sp. nov. from the Nyborg Formation, Vestertana Group, Digermulen Peninsula in Arctic Norway, is a new carbonaceous organ-taxon which consists of stacked tubes with cup-shaped ends. It represents parts of a larger organism (multicellular eukaryote or a colony), likely with greater preservation potential than its other elements. Arrangement of open-ended tubes invites comparison with cells of an epithelial layer present in a variety of eukaryotic clades. This tissue may have benefitted the organism in: avoiding overgrowth, limiting fouling, reproduction, or water filtration. C. digermulense shares characteristics with extant and fossil groups including red algae and their fossils, demosponge larvae and putative sponge fossils, colonial protists, and nematophytes. Regardless of its precise affinity, C. digermulense was a complex and likely benthic marine eukaryote exhibiting cellular differentiation, and a rare occurrence of early multicellularity outside of Konservat-Lagerstatten.

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  • 9.
    Agnas, Axel Jönses Bernard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Non-Independent Mate Choice in Female Humans (Homo sapiens): Progression to the Field 2016Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    There is much evidence that mate-choice decisions made by humans are affected by social/contextual information. Women seem to rate men portrayed in a relationship as more desirable than the same men when portrayed as single. Laboratory studies have found evidence suggesting that human mate choice, as in other species, is dependent on the mate choice decisions made by same-sex rivals. Even though non-independent mate choice is an established and well-studied area of mate choice, very few field studies have been performed. This project aims to test whether women’s evaluation of potential mates desirability is dependent/non-independent of same-sex rivals giving the potential mates sexual interest. This is the first field study performed in a modern human’s natural habitat aiming to test for non- independent mate choice in humans.

    No desirability enhancement effect was found. The possibilities that earlier studies have found an effect that is only present in laboratory environments or have measured effects other than non-independent mate choice are discussed. I find differences in experimental design to be the most likely reason why the present study failed to detect the effect found in previous studies. This field study, the first of its sort, has generated important knowledge for future experimenters, where the most important conclusion is that major limitations in humans ability to register and remember there surrounding should be taken in consideration when designing any field study investigating human mate choice. 

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  • 10.
    Agnolin, Federico L.
    et al.
    Museo Argentino Ciencias Nat Bernardino Rivadavia, Lab Anat Comparada & Evoluc Vertebrados, Buenos Aires, DF, Argentina.; Univ Maimonides, CEBBAD, Dept Ciencias Nat & Antropol, Fundac Hist Nat Felix de Azara, Buenos Aires, DF, Argentina.
    Powell, Jaime E.
    Inst Miguel Lillo, RA-4000 San Miguel De Tucuman, Tucuman, Argentina.; Consejo Nacl Invest Cient & Tecn, RA-1033 Buenos Aires, DF, Argentina.
    Novas, Fernando E.
    Museo Argentino Ciencias Nat Bernardino Rivadavia, Lab Anat Comparada & Evoluc Vertebrados, Buenos Aires, DF, Argentina.; Consejo Nacl Invest Cient & Tecn, RA-1033 Buenos Aires, DF, Argentina.
    Kundrát, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    New alvarezsaurid (Dinosauria, Theropoda) from Latest Cretaceous of North-western Patagonia with associated eggs2012In: Cretaceous research (Print), ISSN 0195-6671, E-ISSN 1095-998X, Vol. 35, p. 33-56Article in journal (Refereed)
    Abstract [en]

    The Alvarezsauridae represents a branch of peculiar basal coelurosaurs with an increasing representationof their Cretaceous radiation distributed worldwide. Here we describe a new member of the group, Bonapartenykus ultimus gen. et sp. nov. from Campanian-Maastrichtian strata of Northern Patagonia, Argentina. Bonapartenykus is represented by a single, incomplete postcranial skeleton. The morphologyof the known skeletal elements suggests close affinities with the previously described taxon from Patagonia, Patagonykus, and both conform to a new clade, here termed Patagonykinae nov. Two incomplete eggs have been discovered in association with the skeletal remains of Bonapartenykus, andseveral clusters of broken eggshells of the same identity were also found in a close proximity. These belong to the new ooparataxon Arriagadoolithus patagoniensis of the new oofamily Arriagadoolithidae, which provides first insights into unique shell microstructure and fungal contamination of eggs laid by alvarezsaurid theropods. The detailed study of the eggs sheds new light on the phylogenetic position of alvarezsaurids within the Theropoda, and the evolution of eggs among Coelurosauria. We suggest thatplesiomorphic alvarezsaurids survived in Patagonia until the latest Cretaceous, whereas these basal forms became extinct elsewhere.

  • 11. Agnès E., Sjöstrand
    et al.
    Per, Sjödin
    Carina, Schlebusch
    Thijessen, Naidoo
    Lucie, Gattepaille
    Nina, Hollfelder
    Torsten, Günther
    Mattias, Jakobsson
    Patterns of local adaptation in AfricansManuscript (preprint) (Other academic)
  • 12. Agnès E., Sjöstrand
    et al.
    Per, Sjödin
    Farhad, Shayimkulov
    Tatiana, Hegay
    Michael G. B., Blum
    Evelyne, Heyer
    Mattias, Jakobsson
    Taste and lifestyle: insights from SNP-chip data.Manuscript (preprint) (Other academic)
  • 13.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Graz, Austria.
    Duenser, Anna
    Karl Franzens Univ Graz, Inst Biol, Graz, Austria.
    Singh, Pooja
    Karl Franzens Univ Graz, Inst Biol, Graz, Austria;Univ Calgary, Inst Biol Sci, Calgary, AB, Canada.
    Gessl, Wolfgang
    Karl Franzens Univ Graz, Inst Biol, Graz, Austria.
    Sturmbauer, Christian
    Karl Franzens Univ Graz, Inst Biol, Graz, Austria.
    Appetite regulating genes may contribute to herbivory versus carnivory trophic divergence in haplochromine cichlids2020In: PeerJ, E-ISSN 2167-8359, Vol. 8, article id e8375Article in journal (Refereed)
    Abstract [en]

    Feeding is a complex behaviour comprised of satiety control, foraging, ingestion and subsequent digestion. Cichlids from the East African Great Lakes are renowned for their diverse trophic specializations, largely predicated on highly variable jaw morphologies. Thus, most research has focused on dissecting the genetic, morphological and regulatory basis of jaw and teeth development in these species. Here for the first time we explore another aspect of feeding, the regulation of appetite related genes that are expressed in the brain and control satiety in cichlid fishes. Using qPCR analysis, we first validate stably expressed reference genes in the brain of six haplochromine cichlid species at the end of larval development prior to foraging. We next evaluate the expression of 16 appetite related genes in herbivorous and carnivorous species from the parallel radiations of Lake Tanganyika, Malawi and Victoria. Interestingly, we find increased expression of two appetite-regulating genes (anorodgenic genes), cart and npy2r, in the brain of carnivorous species in all the three lakes. This supports the notion that appetite gene regulation might play a part in determining trophic niche specialization in divergent cichlid species, already prior to exposure to different diets. Our study contributes to the limited body of knowledge on the neurological circuitry that controls feeding transitions and adaptations in cichlids and other teleosts.

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  • 14.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurene A.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria;Norwegian Univ Sci & Technol, NTNU Univ Museum, Dept Nat Hist, NO-7491 Trondheim, Norway.
    Ziegelbecker, Angelika
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Steiner, Oliver
    Karl Franzens Univ Graz, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Glabonjat, Ronald
    Karl Franzens Univ Graz, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Goessler, Walter
    Karl Franzens Univ Graz, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Hois, Victoria
    Karl Franzens Univ Graz, Inst Mol Biosci, Heinrichstr 31-2, A-8010 Graz, Austria.
    Wagner, Carina
    Karl Franzens Univ Graz, Inst Mol Biosci, Heinrichstr 31-2, A-8010 Graz, Austria.
    Lass, Achim
    Karl Franzens Univ Graz, Inst Mol Biosci, Heinrichstr 31-2, A-8010 Graz, Austria;BioTechMed Graz, A-8010 Graz, Austria.
    Sefc, Kristina M.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Comparative transcriptomics reveals candidate carotenoid color genes in an East African cichlid fish2020In: BMC Genomics, E-ISSN 1471-2164, Vol. 21, article id 54Article in journal (Refereed)
    Abstract [en]

    Background: Carotenoids contribute significantly to animal body coloration, including the spectacular color pattern diversity among fishes. Fish, as other animals, derive carotenoids from their diet. Following uptake, transport and metabolic conversion, carotenoids allocated to body coloration are deposited in the chromatophore cells of the integument. The genes involved in these processes are largely unknown. Using RNA-Sequencing, we tested for differential gene expression between carotenoid-colored and white skin regions of a cichlid fish, Tropheus duboisi "Maswa", to identify genes associated with carotenoid-based integumentary coloration. To control for positional gene expression differences that were independent of the presence/absence of carotenoid coloration, we conducted the same analyses in a closely related population, in which both body regions are white.

    Results: A larger number of genes (n = 50) showed higher expression in the yellow compared to the white skin tissue than vice versa (n = 9). Of particular interest was the elevated expression level of bco2a in the white skin samples, as the enzyme encoded by this gene catalyzes the cleavage of carotenoids into colorless derivatives. The set of genes with higher expression levels in the yellow region included genes involved in xanthophore formation (e.g., pax7 and sox10), intracellular pigment mobilization (e.g., tubb, vim, kif5b), as well as uptake (e.g., scarb1) and storage (e.g., plin6) of carotenoids, and metabolic conversion of lipids and retinoids (e.g., dgat2, pnpla2, akr1b1, dhrs). Triglyceride concentrations were similar in the yellow and white skin regions. Extracts of integumentary carotenoids contained zeaxanthin, lutein and beta-cryptoxanthin as well as unidentified carotenoid structures.

    Conclusion: Our results suggest a role of carotenoid cleavage by Bco2 in fish integumentary coloration, analogous to previous findings in birds. The elevated expression of genes in carotenoid-rich skin regions with functions in retinol and lipid metabolism supports hypotheses concerning analogies and shared mechanisms between these metabolic pathways. Overlaps in the sets of differentially expressed genes (including dgat2, bscl2, faxdc2 and retsatl) between the present study and previous, comparable studies in other fish species provide useful hints to potential carotenoid color candidate genes.

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  • 15.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurène A.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria; Norwegian Univ Sci & Technol, NTNU Univ Museum, Dept Nat Hist, NO-7491 Trondheim, Norway.
    Ziegelbecker, Angelika
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Steiner, Oliver
    Graz Univ, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Goessler, Walter
    Graz Univ, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Sefc, Kristina M.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Expression levels of the tetratricopeptide repeat protein gene ttc39b covary with carotenoid-based skin colour in cichlid fish2020In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 16, no 11, article id 20200629Article in journal (Refereed)
    Abstract [en]

    Carotenoid pigments play a major role in animal body colouration, generating strong interest in the genes involved in the metabolic processes that lead from their dietary uptake to their storage in the integument. Here, we used RNA sequencing (RNA-Seq) to test for differentially expressed genes in a taxonomically replicated design using three pairs of related cichlid fish taxa from the genera Tropheus and Aulonocara. Within each pair, taxa differed in terms of red and yellow body colouration, and high‐performance liquid chromatography (HPLC) analyses of skin extracts revealed different carotenoid profiles and concentrations across the studied taxa. Five genes were differentially expressed in all three yellow–red skin contrasts (dhrsx, nlrc3, tcaf2, urah and ttc39b), but only the tetratricopeptide repeat protein-coding gene ttc39b, whose gene product is linked to mammalian lipid metabolism, was consistently expressed more highly in the red skin samples. The RNA-Seq results were confirmed by quantitative PCR. We propose ttc39b as a compelling candidate gene for variation in animal carotenoid colouration. Since differential expression of ttc39b was correlated with the presence/absence of yellow carotenoids in a previous study, we suggest that ttc39b is more likely associated with the concentration of total carotenoids than with the metabolic formation of red carotenoids.

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  • 16.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Richter, Florian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurene Alicia
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sefc, Kristina M.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 9052Article in journal (Refereed)
    Abstract [en]

    Comparative analyses of gene regulation inform about the molecular basis of phenotypic trait evolution. Here, we address a fin shape phenotype that evolved multiple times independently across teleost fish, including several species within the family Cichlidae. In a previous study, we proposed a gene regulatory network (GRN) involved in the formation and regeneration of conspicuous filamentous elongations adorning the unpaired fins of the Neolamprologus brichardi. Here, we tested the members of this network in the blockhead cichlid, Steatocranus casuarius, which displays conspicuously elongated dorsal and moderately elongated anal fins. Our study provided evidence for differences in the anatomy of fin elongation and suggested gene regulatory divergence between the two cichlid species. Only a subset of the 20 genes tested in S. casuarius showed the qPCR expression patterns predicted from the GRN identified in N. brichardi, and several of the gene-by-gene expression correlations differed between the two cichlid species. In comparison to N. brichardi, gene expression patterns in S. casuarius were in better (but not full) agreement with gene regulatory interactions inferred in zebrafish. Within S. casuarius, the dorsoventral asymmetry in ornament expression was accompanied by differences in gene expression patterns, including potential regulatory differentiation, between the anal and dorsal fin.

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  • 17.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Singh, Pooja
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Duenser, Anna
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gessl, Wolfgang
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sturmbauer, Christian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging2019In: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 19, article id 150Article in journal (Refereed)
    Abstract [en]

    BackgroundUnderstanding how variation in gene expression contributes to morphological diversity is a major goal in evolutionary biology. Cichlid fishes from the East African Great lakes exhibit striking diversity in trophic adaptations predicated on the functional modularity of their two sets of jaws (oral and pharyngeal). However, the transcriptional basis of this modularity is not so well understood, as no studies thus far have directly compared the expression of genes in the oral and pharyngeal jaws. Nor is it well understood how gene expression may have contributed to the parallel evolution of trophic morphologies across the replicate cichlid adaptive radiations in Lake Tanganyika, Malawi and Victoria.ResultsWe set out to investigate the role of gene expression divergence in cichlid fishes from these three lakes adapted to herbivorous and carnivorous trophic niches. We focused on the development stage prior to the onset of exogenous feeding that is critical for understanding patterns of gene expression after oral and pharyngeal jaw skeletogenesis, anticipating environmental cues. This framework permitted us for the first time to test for signatures of gene expression underlying jaw modularity in convergent eco-morphologies across three independent adaptive radiations. We validated a set of reference genes, with stable expression between the two jaw types and across species, which can be important for future studies of gene expression in cichlid jaws. Next we found evidence of modular and non-modular gene expression between the two jaws, across different trophic niches and lakes. For instance, prdm1a, a skeletogenic gene with modular anterior-posterior expression, displayed higher pharyngeal jaw expression and modular expression pattern only in carnivorous species. Furthermore, we found the expression of genes in cichlids jaws from the youngest Lake Victoria to exhibit low modularity compared to the older lakes.ConclusionOverall, our results provide cross-species transcriptional comparisons of modularly-regulated skeletogenic genes in the two jaw types, implicating expression differences which might contribute to the formation of divergent trophic morphologies at the stage of larval independence prior to foraging.

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  • 18.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Singh, Pooja
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurene Alicia
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gessl, Wolfgang
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sturmbauer, Christian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Maternal mRNA input of growth and stress-response-related genes in cichlids in relation to egg size and trophic specialization2018In: EvoDevo, E-ISSN 2041-9139, Vol. 9, article id 23Article in journal (Refereed)
    Abstract [en]

    Background: Egg size represents an important form of maternal effect determined by a complex interplay of long-term adaptation and short-term plasticity balancing egg size with brood size. Haplochromine cichlids are maternal mouthbrooders showing differential parental investment in different species, manifested in great variation in egg size, brood size and duration of maternal care. Little is known about maternally determined molecular characters of eggs in fishes and their relation to egg size and trophic specialization. Here we investigate maternal mRNA inputs of selected growth- and stress-related genes in eggs of mouthbrooding cichlid fishes adapted to different trophic niches from Lake Tanganyika, Lake Malawi, Lake Victoria and compare them to their riverine allies.

    Results: We first identified two reference genes, atf7ip and mid1ip1, to be suitable for cross-species quantification of mRNA abundance via qRT-PCR in the cichlid eggs. Using these reference genes, we found substantial variation in maternal mRNA input for a set of candidate genes related to growth and stress response across species and lakes. We observed negative correlation of mRNA abundance between two of growth hormone receptor paralogs (ghr1 and ghr2) across all haplochromine cichlid species which also differentiate the species in the two younger lakes, Malawi and Lake Victoria, from those in Lake Tanganyika and ancestral riverine species. Furthermore, we found correlations between egg size and maternal mRNA abundance of two growth-related genes igf2 and ghr2 across the haplochromine cichlids as well as distinct clustering of the species based on their trophic specialization using maternal mRNA abundance of five genes (ghr1, ghr2, igf2, gr and sgk1).

    Conclusions: These findings indicate that variations in egg size in closely related cichlid species can be linked to differences in maternal RNA deposition of key growth-related genes. In addition, the cichlid species with contrasting trophic specialization deposit different levels of maternal mRNAs in their eggs for particular growth-related genes; however, it is unclear whether such differences contribute to differential morphogenesis at later stages of development. Our results provide first insights into this aspect of gene activation, as a basis for future studies targeting their role during ecomorphological specialization and adaptive radiation.

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  • 19.
    Ah-King, Malin
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Centre for Gender Research. Dept Ecol & Evolutionary Biol, 621 Charles E Young Dr S, Los Angeles, CA 90095 USA.;Stockholm Univ, Dept Ethnol Hist Relig & Gender Studies, Univ Vagen 10 E, SE-10691 Stockholm, Sweden..
    Gowaty, Patricia Adair
    Dept Ecol & Evolutionary Biol, 621 Charles E Young Dr S, Los Angeles, CA 90095 USA.;Smithsonian Trop Res Inst, DPO, Box 0948,AA 34002-9998, Washington, DC USA.;Univ Calif Los Angeles, Inst Environm & Sustainabil, Los Angeles, CA 90095 USA..
    A conceptual review of mate choice: stochastic demography, within-sex phenotypic plasticity, and individual flexibility2016In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 6, no 14, p. 4607-4642Article, review/survey (Refereed)
    Abstract [en]

    Mate choice hypotheses usually focus on trait variation of chosen individuals. Recently, mate choice studies have increasingly attended to the environmental circumstances affecting variation in choosers' behavior and choosers' traits. We reviewed the literature on phenotypic plasticity in mate choice with the goal of exploring whether phenotypic plasticity can be interpreted as individual flexibility in the context of the switch point theorem, SPT (Gowaty and Hubbell ). We found >3000 studies; 198 were empirical studies of within-sex phenotypic plasticity, and sixteen showed no evidence of mate choice plasticity. Most studies reported changes from choosy to indiscriminate behavior of subjects. Investigators attributed changes to one or more causes including operational sex ratio, adult sex ratio, potential reproductive rate, predation risk, disease risk, chooser's mating experience, chooser's age, chooser's condition, or chooser's resources. The studies together indicate that choosiness of potential mates is environmentally and socially labile, that is, induced - not fixed - in the choosy sex with results consistent with choosers' intrinsic characteristics or their ecological circumstances mattering more to mate choice than the traits of potential mates. We show that plasticity-associated variables factor into the simpler SPT variables. We propose that it is time to complete the move from questions about within-sex plasticity in the choosy sex to between- and within-individual flexibility in reproductive decision-making of both sexes simultaneously. Currently, unanswered empirical questions are about the force of alternative constraints and opportunities as inducers of individual flexibility in reproductive decision-making, and the ecological, social, and developmental sources of similarities and differences between individuals. To make progress, we need studies (1) of simultaneous and symmetric attention to individual mate preferences and subsequent behavior in both sexes, (2) controlled for within-individual variation in choice behavior as demography changes, and which (3) report effects on fitness from movement of individual's switch points.

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  • 20.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    A comparative genomic framework for the fish-tetrapod transition2021In: Science China Life Sciences, ISSN 1674-7305, E-ISSN 1869-1889, Vol. 64, no 4, p. 664-666Article in journal (Other academic)
  • 21.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Follow the footprints and mind the gaps: a new look at the origin of tetrapods2019In: Earth and environmental science transactions of the Royal Society of Edinburgh, ISSN 1755-6910, E-ISSN 1755-6929, Vol. 109, no 1-2, p. 115-137Article in journal (Refereed)
    Abstract [en]

    The hypothesis that tetrapods evolved from elpistostegids during the Frasnian, in a predominantly aquatic context, has been challenged by the discovery of Middle Devonian tetrapod trackways predating the earliest body fossils of both elpistostegids and tetrapods. Here I present a new hypothesis based on an overview of the trace fossil and body fossil evidence. The trace fossils demonstrate that tetrapods were capable of performing subaerial lateral sequence walks before the end of the Middle Devonian. The derived morphological characters of elpistostegids and Devonian tetrapods are related to substrate locomotion, weight support and aerial vision, and thus to terrestrial competence, but the retention of lateral-line canals, gills and fin rays shows that they remained closely tied to the water. Elpistostegids and tetrapods both evolved no later than the beginning of the Middle Devonian. The earliest tetrapod records come from inland river basins, sabkha plains and ephemeral coastal lakes that preserve few, if any, body fossils; contemporary elpistostegids occur in deltas and the lower reaches of permanent rivers where body fossils are preserved. During the Frasnian, elpistostegids disappear and these riverine-deltaic environments are colonised by tetrapods. This replacement has, in the past, been misinterpreted as the origin of tetrapods.

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  • 22.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jennifer Clack (1947–2020): Palaeontologist who described how vertebrates moved from water to land2020In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 580, no 7805, p. 587-587Article in journal (Other (popular science, discussion, etc.))
  • 23.
    Ahlberg, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Beznosov, P. A.
    Russian Acad Sci, Inst Geol, FRC Komi Sci Ctr, Ural Branch, Syktyvkar 167982, Russia..
    The Significance of the Devonian Tetrapods of Timan2022In: Paleontological journal, ISSN 0031-0301, E-ISSN 1555-6174, Vol. 56, p. 1029-1031Article in journal (Refereed)
    Abstract [en]

    Brief information on the recently described Parmastega and newly discovered unpublished tetrapod material from the Devonian sequence of Timan is given. The significance of these discoveries is discussed.

  • 24.
    Ahlberg, Per E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Clack, Jennifer A.
    Univ Museum Zool Cambridge, Downing St, Cambridge CB2 3EJ, England..
    The smallest known Devonian tetrapod shows unexpectedly derived features2020In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 7, no 4, article id 192117Article in journal (Refereed)
    Abstract [en]

    A new genus and species of Devonian tetrapod, Brittagnathus minutus gen. et sp. nov., is described from a single complete right lower jaw ramus recovered from the Acanthostega mass-death deposit in the upper part of the Britta Dal Formation (upper Famennian) of Stensio Bjerg, Gauss Peninsula, East Greenland. Visualization by propagation phase contrast synchrotron microtomography allows a complete digital dissection of the specimen. With a total jaw ramus length of 44.8 mm, Brittagnathus is by far the smallest Devonian tetrapod described to date. It differs from all previously known Devonian tetrapods in having only a fang pair without a tooth row on the anterior coronoid and a large posterior process on the posterior coronoid. The presence of an incipient surangular crest and a concave prearticular margin to the adductor fossa together cause the fossa to face somewhat mesially, reminiscent of the condition in Carboniferous tetrapods. A phylogenetic analysis places Brittagnathus crownward to other Devonian tetrapods, adjacent to the Tournaisian genus Pederpes. Together with other recent discoveries, it suggests that diversification of 'Carboniferous-grade' tetrapods had already begun before the end of the Devonian and that the group was not greatly affected by the end-Devonian mass extinction.

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  • 25.
    Ahnesjö, Ingrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Brealey, Jaelle C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Günter, Katerina P.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Centre for Gender Research.
    Martinossi‑Allibert, Ivain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Morinay, Jennifer
    Siljestam, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Stångberg, Josefine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Vasconcelos, Paula
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Considering Gender‑Biased Assumptions in Evolutionary Biology2020In: Evolutionary biology, ISSN 0071-3260, E-ISSN 1934-2845, Vol. 47, p. 1-5Article in journal (Refereed)
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  • 26.
    Akiyama, Reiko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Life History and Tolerance and Resistance against Herbivores in Natural Populations of Arabidopsis thaliana2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, I combined observational studies with field and greenhouse experiments to examine selection on life history traits and variation in tolerance and resistance against herbivores in natural populations of the annual herb Arabidopsis thaliana in its native range. I investigated (1) phenotypic selection on flowering time and plant size, (2) the effects of timing of germination on plant fitness, (3) the effect of leaf damage on seed production, and (4) correlations between resistance against a specialist and a generalist insect herbivore.

    In all three study populations, flowering time was negatively related to plant fitness, but in only one of the populations, significant selection on flowering time was detected when controlling for size prior to the flowering season. The results show that correlations between flowering time and plant fecundity may be confounded by variation in plant size prior to the reproductive season.

    A field experiment detected conflicting selection on germination time: Early germination was associated with low seedling survival, but also with large leaf rosette before winter and high survival and fecundity among established plants. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination, and that the optimal timing of germination should vary in space and time as a function of the relative strength of selection acting during different life-history stages.

    Experimental leaf damage demonstrated that tolerance to damage was lowest among vegetative plants early in the season, and highest among flowering plants later in the season. Given similar damage levels, leaf herbivores feeding on plants before flowering should thus exert stronger selection on defence traits than those feeding on plants during flowering.

    Resistance against larval feeding by the specialist Plutella xylostella was negatively correlated with resistance against larval feeding by the generalist Mamestra brassicae and with resistance against oviposition by P. xylostella when variation in resistance was examined within and among two Swedish and two Italian A. thaliana populations. The results suggest that negative correlations between resistance against different herbivores and different life-history stages of herbivores may contribute to the maintenance of genetic variation in resistance.

    List of papers
    1. Selection on flowering time in three natural populations of Arabidopsis thaliana
    Open this publication in new window or tab >>Selection on flowering time in three natural populations of Arabidopsis thaliana
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Evolutionary Biology Botany
    Research subject
    Biology with specialization in Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-159506 (URN)
    Funder
    Swedish Research Council
    Available from: 2011-10-06 Created: 2011-10-03 Last updated: 2011-11-10
    2. Conflicting selection on the timing of germination in a natural population of Arabidopsis thaliana
    Open this publication in new window or tab >>Conflicting selection on the timing of germination in a natural population of Arabidopsis thaliana
    2014 (English)In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, no 1, p. 193-199Article in journal (Refereed) Published
    Abstract [en]

    The timing of germination is a key life-history trait that may strongly influence plant fitness and that sets the stage for selection on traits expressed later in the life cycle. In seasonal environments, the period favourable for germination and the total length of the growing season are limited. The optimal timing of germination may therefore be governed by conflicting selection through survival and fecundity. We conducted a field experiment to examine the effects of timing of germination on survival, fecundity and overall fitness in a natural population of the annual herb Arabidopsis thaliana in north-central Sweden. Seedlings were transplanted at three different times in late summer and in autumn covering the period of seed germination in the study population. Early germination was associated with low seedling survival, but also with high survival and fecundity among established plants. The advantages of germinating early more than balanced the disadvantage and selection favoured early germination. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination and that the optimal timing of germination should vary in space and time as a function of the direction and strength of selection acting during different life-history stages.

    National Category
    Ecology Evolutionary Biology Botany
    Research subject
    Biology with specialization in Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-159664 (URN)10.1111/jeb.12293 (DOI)000329254500018 ()
    Funder
    Swedish Research Council
    Available from: 2011-10-06 Created: 2011-10-06 Last updated: 2022-01-28Bibliographically approved
    3. Magnitude and timing of leaf damage affect seed production in a natural population of Arabidopsis thaliana (Brassicaceae)
    Open this publication in new window or tab >>Magnitude and timing of leaf damage affect seed production in a natural population of Arabidopsis thaliana (Brassicaceae)
    2012 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 7, no 1, p. e30015-Article in journal (Refereed) Published
    Abstract [en]

    Background: The effect of herbivory on plant fitness varies widely. Understanding the causes of this variation is of considerable interest because of its implications for plant population dynamics and trait evolution. We experimentally defoliated the annual herb Arabidopsis thaliana in a natural population in Sweden to test the hypotheses that (a) plant fitness decreases with increasing damage, (b) tolerance to defoliation is lower before flowering than during flowering, and (c) defoliation before flowering reduces number of seeds more strongly than defoliation during flowering, but the opposite is true for effects on seed size.

    Methodology/Principal Findings: In a first experiment, between 0 and 75% of the leaf area was removed in May from plants that flowered or were about to start flowering. In a second experiment, 0, 25%, or 50% of the leaf area was removed from plants on one of two occasions, in mid April when plants were either in the vegetative rosette or bolting stage, or in mid May when plants were flowering. In the first experiment, seed production was negatively related to leaf area removed, and at the highest damage level, also mean seed size was reduced. In the second experiment, removal of 50% of the leaf area reduced seed production by 60% among plants defoliated early in the season at the vegetative rosettes, and by 22% among plants defoliated early in the season at the bolting stage, but did not reduce seed output of plants defoliated one month later. No seasonal shift in the effect of defoliation on seed size was detected.

    Conclusions/Significance: The results show that leaf damage may reduce the fitness of A. thaliana, and suggest that in this population leaf herbivores feeding on plants before flowering should exert stronger selection on defence traits than those feeding on plants during flowering, given similar damage levels.

    National Category
    Ecology Evolutionary Biology Botany
    Research subject
    Biology with specialization in Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-159665 (URN)10.1371/journal.pone.0030015 (DOI)000301457200028 ()
    Funder
    Swedish Research Council
    Available from: 2011-10-06 Created: 2011-10-06 Last updated: 2021-06-14Bibliographically approved
    4. Genetic variation in leaf morphology and resistance against specialist and generalist insect herbivores in natural populations of Arabidopsis thaliana
    Open this publication in new window or tab >>Genetic variation in leaf morphology and resistance against specialist and generalist insect herbivores in natural populations of Arabidopsis thaliana
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Evolutionary Biology Botany
    Research subject
    Biology with specialization in Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-159685 (URN)
    Funder
    Swedish Research Council
    Available from: 2011-10-06 Created: 2011-10-06 Last updated: 2011-11-10
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  • 27.
    Akiyama, Reiko
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Noack, Sibylle
    Department of Zoology, Stockholm University.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genetic variation in leaf morphology and resistance against specialist and generalist insect herbivores in natural populations of Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 28.
    Akiyama, Reiko
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conflicting selection on the timing of germination in a natural population of Arabidopsis thaliana2014In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, no 1, p. 193-199Article in journal (Refereed)
    Abstract [en]

    The timing of germination is a key life-history trait that may strongly influence plant fitness and that sets the stage for selection on traits expressed later in the life cycle. In seasonal environments, the period favourable for germination and the total length of the growing season are limited. The optimal timing of germination may therefore be governed by conflicting selection through survival and fecundity. We conducted a field experiment to examine the effects of timing of germination on survival, fecundity and overall fitness in a natural population of the annual herb Arabidopsis thaliana in north-central Sweden. Seedlings were transplanted at three different times in late summer and in autumn covering the period of seed germination in the study population. Early germination was associated with low seedling survival, but also with high survival and fecundity among established plants. The advantages of germinating early more than balanced the disadvantage and selection favoured early germination. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination and that the optimal timing of germination should vary in space and time as a function of the direction and strength of selection acting during different life-history stages.

    Download full text (pdf)
    Akiyama & Ågren JEB 2014
  • 29.
    Akiyama, Reiko
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Magnitude and timing of leaf damage affect seed production in a natural population of Arabidopsis thaliana (Brassicaceae)2012In: PLOS ONE, E-ISSN 1932-6203, Vol. 7, no 1, p. e30015-Article in journal (Refereed)
    Abstract [en]

    Background: The effect of herbivory on plant fitness varies widely. Understanding the causes of this variation is of considerable interest because of its implications for plant population dynamics and trait evolution. We experimentally defoliated the annual herb Arabidopsis thaliana in a natural population in Sweden to test the hypotheses that (a) plant fitness decreases with increasing damage, (b) tolerance to defoliation is lower before flowering than during flowering, and (c) defoliation before flowering reduces number of seeds more strongly than defoliation during flowering, but the opposite is true for effects on seed size.

    Methodology/Principal Findings: In a first experiment, between 0 and 75% of the leaf area was removed in May from plants that flowered or were about to start flowering. In a second experiment, 0, 25%, or 50% of the leaf area was removed from plants on one of two occasions, in mid April when plants were either in the vegetative rosette or bolting stage, or in mid May when plants were flowering. In the first experiment, seed production was negatively related to leaf area removed, and at the highest damage level, also mean seed size was reduced. In the second experiment, removal of 50% of the leaf area reduced seed production by 60% among plants defoliated early in the season at the vegetative rosettes, and by 22% among plants defoliated early in the season at the bolting stage, but did not reduce seed output of plants defoliated one month later. No seasonal shift in the effect of defoliation on seed size was detected.

    Conclusions/Significance: The results show that leaf damage may reduce the fitness of A. thaliana, and suggest that in this population leaf herbivores feeding on plants before flowering should exert stronger selection on defence traits than those feeding on plants during flowering, given similar damage levels.

    Download full text (pdf)
    fulltext
  • 30.
    Akiyama, Reiko
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Selection on flowering time in three natural populations of Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 31.
    Al Jewari, Caesar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    An excavate root for the eukaryote tree of life2023In: Science Advances, ISSN 2375-2548, Vol. 9, no 17, article id eade4973Article in journal (Other academic)
    Abstract [en]

    Much of the higher-order phylogeny of eukaryotes is well resolved, but the root remains elusive. We assembled a dataset of 183 eukaryotic proteins of archaeal ancestry to test this root. The resulting phylogeny identifies four lineages of eukaryotes currently classified as “Excavata” branching separately at the base of the tree. Thus, Parabasalia appear as the first major branch of eukaryotes followed sequentially by Fornicata, Preaxostyla, and Discoba. All four excavate branch points receive full statistical support from analyses with commonly used evolutionary models, a protein structure partition model that we introduce here, and various controls for deep phylogeny artifacts. The absence of aerobic mitochondria in Parabasalia, Fornicata, and Preaxostyla suggests that modern eukaryotes arose under anoxic conditions, probably much earlier than expected, and without the benefit of mitochondrial respiration.

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  • 32.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Little, Chelsea J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jagerbrand, Annika K.
    Molau, Ulf
    Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change2014In: PeerJ, E-ISSN 2167-8359, Vol. 2, p. e406-Article in journal (Refereed)
    Abstract [en]

    We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years) responses are good predictors for medium-term (7 years) changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-termresponses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both), different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity-diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant-plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the Arctic.

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    fulltext
  • 33.
    Alavioon, Ghazal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Haploid selection in animals: Exploring the fitness consequences and underlying mechanisms2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A consequence of sexual reproduction in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid gametic phases. While our focus in evolutionary biology is on selection during the diploid phase, we know relatively little about selection occurring during the haploid gametic stage. This is particularly true in predominantly diploid animals, where gene expression and hence selection have long been thought to be absent in haploid cells like gametes and particularly sperm. During my PhD, I tested the idea of selection during the haploid gametic phase using zebrafish Danio rario as a study species. I combined a large-scale selection experiment over three generations with fitness assays and next-generation sequencing to assess the importance of haploid selection. We measured offspring fitness in all three generations.  In addition, we compared gene expression in brain and testes of F1 and F3 adult male from each treatment by RNA sequencing. We found that offspring sired by longer-lived sperm showed higher survival rate and higher early- and late-life reproductive fitness compared to offspring sired by shorter-lived sperm. We also found differentially expressed genes between the two treatments with functions in metabolic and developmental pathways. These findings suggest that the observed fitness differences to be caused by small expression changes in many basic genes. We also tested for a genetic underpinning of the selected sperm phenotypes and identified allelic differences across the entire genome. Finally, we investigated the additive genetic component and parental effect of different sperm phenotypes. We found generally low additive genetic variation and high parental effects on sperm performance traits. In conclusion, this thesis provides evidence that the phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness throughout life and provides a clear link between sperm phenotype and offspring fitness and between sperm phenotype and sperm genotype.

    List of papers
    1. Haploid selection within a single ejaculate increases offspring fitness
    Open this publication in new window or tab >>Haploid selection within a single ejaculate increases offspring fitness
    Show others...
    2017 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, no 30, p. 8053-8058Article in journal (Refereed) Published
    Abstract [en]

    An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring. Using the zebrafish Danio rerio, we show that selection on phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness. Longer-lived sperm sired embryos with increased survival and a reduced number of apoptotic cells, and adult male offspring exhibited higher fitness. The effect on embryo viability was carried over into the second generation without further selection and was equally strong in both sexes. Sperm pools selected by motile phenotypes differed genetically at numerous sites throughout the genome. Our findings clearly link within-ejaculate variation in sperm phenotype to offspring fitness and sperm genotype in a vertebrate and have major implications for adaptive evolution.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-320335 (URN)10.1073/pnas.1705601114 (DOI)000406189900080 ()28698378 (PubMedID)
    Funder
    Swedish Research CouncilEU, European Research Council
    Available from: 2017-04-19 Created: 2017-04-19 Last updated: 2022-01-29Bibliographically approved
    2. Within-ejaculate selection for sperm longevity reduces male reproductive ageing
    Open this publication in new window or tab >>Within-ejaculate selection for sperm longevity reduces male reproductive ageing
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Males produce numerous sperm in the single ejaculate that greatly outnumber their potential egg targets. Recent studies found that phenotypic variation among sperm in the single ejaculate of a male reflects the phenotype and the genotype of the resulting offspring. Specifically, within-ejaculate sperm selection (WESS) for sperm longevity increased the performance of the resulting offspring in several key life-history traits in early-life. Because increased early-life reproductive performance often correlates with rapid ageing, it is possible that WESS increases early-life fitness at the cost of accelerated senescence. Alternatively, WESS can improve offspring quality throughout the life cycle, including reduced age-specific deterioration. We found that WESS for sperm longevity reduced age-specific deterioration of male fertility and embryo survival, while there is no effect on fertilization success. Remarkably, we found opposing effect of WESS on female fecundity, where selection for sperm longevity resulted in increased early-life performance followed by a slow decline, while unselected controls started low but increased their fecundity with age. Intriguingly, WESS also reduced the age-specific decline in fertilization success in females, suggesting that selection for sperm longevity improves at least some aspects of female reproductive ageing. These results demonstrate that within-ejaculate variation in sperm phenotype contributes to individual variation in animal life histories in the two sexes and have important implications for assisted fertilization programs in livestock and humans. 

    Keywords
    Ageing, Reproductive Success, Sperm Selection, Sperm Competition, Senescence
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-350186 (URN)
    Available from: 2018-05-07 Created: 2018-05-07 Last updated: 2018-05-07
    3. The fitness consequences of selection among sperm within an ejaculate across generations
    Open this publication in new window or tab >>The fitness consequences of selection among sperm within an ejaculate across generations
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The evolution of a biphasic life cycle with alternating diploid and haploid phases is a necessary consequence of sexual reproduction in eukaryotes. Selection in each of the phases may have far reaching consequences for many evolutionary processes. While our focus in evolutionary biology lies mainly on selection during the diploid phase, we know relatively little about the role and consequences of selection occurring during the haploid gametic stage. This is particularly true in predominantly diploid animals where the haploid gametic phase is very short. To test the importance of haploid selection in animals, we performed a large-scale selection experiment with selection acting on haploid sperm. We selected on sperm longevity within an ejaculate and tested the effects of such selection over three generation. We performed fitness assays for every generation and found that offspring sired by longer-lived sperm generally exhibit higher fitness from early development into adulthood compared to offspring sired by their shorter-lived sibling sperm in all three generations. These fitness effects were carried over into the second generation without further selection in all three generations. Moreover, using RNA sequencing, we assessed differences in tissue specific gene expression between the offspring sired by the two sperm phenotypes in generation F1 and F3. The transcriptomes in both tissues differed significantly between the two treatments. Many very basic housekeeping genes involved in metabolism and development showed small differences in expression in both tissues. Our study provides solid evidence for the far-reaching consequences of selection on different sperm within a single ejaculate in three consecutive generations, and offers exciting new insights into the possible underlying mechanisms. Our results further highlight the importance of selection at the haploid gametic stages for fundamental evolutionary processes and assisted fertilization technologies.

    Keywords
    Haploid selection, sperm selection, offspring fitness, gene expression
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-350190 (URN)
    Available from: 2018-05-07 Created: 2018-05-07 Last updated: 2018-05-07
    4. Sperm performance traits exhibit low additive genetic component and strong parental effects in external fertilizer
    Open this publication in new window or tab >>Sperm performance traits exhibit low additive genetic component and strong parental effects in external fertilizer
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Despite their key role in determining reproductive success and with that Darwinian fitness, the heritability and underlying additive genetic variance of reproductive traits is still not fully understood. While some traits show relatively high genetic variance, others show very low genetic variance, which is particularly true for complex non-morphological traits. In line with these general patterns, morphological sperm traits show surprisingly high heritability, whereas heritability reported for sperm quality and performance traits generally is lower. A possible explanation for this is the general notion that more fitness related traits show lower levels of additive genetic variance and heritability. We investigated the additive genetic variance and heritability of sperm swimming velocity, the percentage of motile sperm, sperm concentration in the ejaculate and sperm longevity in the externally fertilizing zebrafish Danio rerio. All sperm traits showed low but significant additive genetic variance and high parental components. While the additive genetic variance was significant it was lower than reported in many other studies. A possible explanation for this is that in externally fertilizing species, sperm traits are the prime determinant of fertilization success and high plasticity is crucial for swift adaptations to changes in the environmental conditions such as competition but also water temperature and currents. Given that this is the first study looking into the heritability of sperm traits in an external fertilizer it will be interesting to understand, whether this is true for other externally fertilizing species and taxa.

    Keywords
    additive genetic, parental effect, sperm traits, reproduction
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-350191 (URN)
    Available from: 2018-05-07 Created: 2018-05-07 Last updated: 2018-06-01
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  • 34.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Baños-Villalba, Adrian
    University Pablo de Olavide, Ctra.
    Schielzeth, Holger
    Friedrich Schiller University Jena.
    Immler, Simone
    University of East Anglia.
    Sperm performance traits exhibit low additive genetic component and strong parental effects in external fertilizerManuscript (preprint) (Other academic)
    Abstract [en]

    Despite their key role in determining reproductive success and with that Darwinian fitness, the heritability and underlying additive genetic variance of reproductive traits is still not fully understood. While some traits show relatively high genetic variance, others show very low genetic variance, which is particularly true for complex non-morphological traits. In line with these general patterns, morphological sperm traits show surprisingly high heritability, whereas heritability reported for sperm quality and performance traits generally is lower. A possible explanation for this is the general notion that more fitness related traits show lower levels of additive genetic variance and heritability. We investigated the additive genetic variance and heritability of sperm swimming velocity, the percentage of motile sperm, sperm concentration in the ejaculate and sperm longevity in the externally fertilizing zebrafish Danio rerio. All sperm traits showed low but significant additive genetic variance and high parental components. While the additive genetic variance was significant it was lower than reported in many other studies. A possible explanation for this is that in externally fertilizing species, sperm traits are the prime determinant of fertilization success and high plasticity is crucial for swift adaptations to changes in the environmental conditions such as competition but also water temperature and currents. Given that this is the first study looking into the heritability of sperm traits in an external fertilizer it will be interesting to understand, whether this is true for other externally fertilizing species and taxa.

  • 35.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Cabrera, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    LeChatelier, Magali
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Maklakov, Alexei A.
    University of East Anglia.
    Immler, Simone
    University of East Anglia.
    Within-ejaculate selection for sperm longevity reduces male reproductive ageingManuscript (preprint) (Other academic)
    Abstract [en]

    Males produce numerous sperm in the single ejaculate that greatly outnumber their potential egg targets. Recent studies found that phenotypic variation among sperm in the single ejaculate of a male reflects the phenotype and the genotype of the resulting offspring. Specifically, within-ejaculate sperm selection (WESS) for sperm longevity increased the performance of the resulting offspring in several key life-history traits in early-life. Because increased early-life reproductive performance often correlates with rapid ageing, it is possible that WESS increases early-life fitness at the cost of accelerated senescence. Alternatively, WESS can improve offspring quality throughout the life cycle, including reduced age-specific deterioration. We found that WESS for sperm longevity reduced age-specific deterioration of male fertility and embryo survival, while there is no effect on fertilization success. Remarkably, we found opposing effect of WESS on female fecundity, where selection for sperm longevity resulted in increased early-life performance followed by a slow decline, while unselected controls started low but increased their fecundity with age. Intriguingly, WESS also reduced the age-specific decline in fertilization success in females, suggesting that selection for sperm longevity improves at least some aspects of female reproductive ageing. These results demonstrate that within-ejaculate variation in sperm phenotype contributes to individual variation in animal life histories in the two sexes and have important implications for assisted fertilization programs in livestock and humans. 

  • 36.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Garcia, Andrea Cabrera
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    LeChatelier, Magali
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Maklakov, Alex A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich, Norfolk, England.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich, Norfolk, England.
    Selection for longer lived sperm within ejaculate reduces reproductive ageing in offspring2019In: Evolution Letters, E-ISSN 2056-3744, Vol. 3, no 2, p. 198-206Article in journal (Refereed)
    Abstract [en]

    Males produce numerous sperm in a single ejaculate that greatly outnumber their potential egg targets. Recent studies found that phenotypic and genotypic variation among sperm in a single ejaculate of a male affects the fitness and performance of the resulting offspring. Specifically, within-ejaculate sperm selection for sperm longevity increased the performance of the resulting offspring in several key life-history traits in early life. Because increased early-life reproductive performance often correlates with rapid ageing, it is possible that within-ejaculate sperm selection increases early-life fitness at the cost of accelerated senescence. Alternatively, within-ejaculate sperm selection could improve offspring quality throughout the life cycle, including reduced age-specific deterioration. We tested the two alternative hypotheses in an experimental setup using zebrafish Danio rerio. We found that within-ejaculate sperm selection for sperm longevity reduced age-specific deterioration of fecundity and offspring survival but had no effect on fertilization success in males. Remarkably, we found an opposing effect of within-ejaculate sperm selection on female fecundity, where selection for sperm longevity resulted in increased early-life performance followed by a slow decline, while females sired by unselected sperm started low but increased their fecundity with age. Intriguingly, within-ejaculate sperm selection also reduced the age-specific decline in fertilization success in females, suggesting that selection for sperm longevity improves at least some aspects of female reproductive ageing. These results demonstrate that within-ejaculate variation in sperm phenotype contributes to individual variation in animal life histories in the two sexes and may have important implications for assisted fertilization programs in livestock and humans.

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  • 37.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hotzy, Cosima
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nakhro, Khriezhanuo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rudolf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zajitschek, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Spanish Natl Res Council, Donana Biol Stn, Seville 41092, Spain.
    Maklakov, Alex A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ East Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ East Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
    Haploid selection within a single ejaculate increases offspring fitness2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, no 30, p. 8053-8058Article in journal (Refereed)
    Abstract [en]

    An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring. Using the zebrafish Danio rerio, we show that selection on phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness. Longer-lived sperm sired embryos with increased survival and a reduced number of apoptotic cells, and adult male offspring exhibited higher fitness. The effect on embryo viability was carried over into the second generation without further selection and was equally strong in both sexes. Sperm pools selected by motile phenotypes differed genetically at numerous sites throughout the genome. Our findings clearly link within-ejaculate variation in sperm phenotype to offspring fitness and sperm genotype in a vertebrate and have major implications for adaptive evolution.

  • 38.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Roy M, Francis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Wyszkowska, Julia
    Jagiellonian University.
    Immler, Simone
    University of East Anglia.
    The fitness consequences of selection among sperm within an ejaculate across generationsManuscript (preprint) (Other academic)
    Abstract [en]

    The evolution of a biphasic life cycle with alternating diploid and haploid phases is a necessary consequence of sexual reproduction in eukaryotes. Selection in each of the phases may have far reaching consequences for many evolutionary processes. While our focus in evolutionary biology lies mainly on selection during the diploid phase, we know relatively little about the role and consequences of selection occurring during the haploid gametic stage. This is particularly true in predominantly diploid animals where the haploid gametic phase is very short. To test the importance of haploid selection in animals, we performed a large-scale selection experiment with selection acting on haploid sperm. We selected on sperm longevity within an ejaculate and tested the effects of such selection over three generation. We performed fitness assays for every generation and found that offspring sired by longer-lived sperm generally exhibit higher fitness from early development into adulthood compared to offspring sired by their shorter-lived sibling sperm in all three generations. These fitness effects were carried over into the second generation without further selection in all three generations. Moreover, using RNA sequencing, we assessed differences in tissue specific gene expression between the offspring sired by the two sperm phenotypes in generation F1 and F3. The transcriptomes in both tissues differed significantly between the two treatments. Many very basic housekeeping genes involved in metabolism and development showed small differences in expression in both tissues. Our study provides solid evidence for the far-reaching consequences of selection on different sperm within a single ejaculate in three consecutive generations, and offers exciting new insights into the possible underlying mechanisms. Our results further highlight the importance of selection at the haploid gametic stages for fundamental evolutionary processes and assisted fertilization technologies.

  • 39.
    Albrecht, Lisa M.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Antibiotic Resistance: Selection in the Presence of Metals and Antimicrobials2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The external environment is complex: Antibiotics, metals and antimicrobials do not exist in isolation but in mixtures. Human activities such as animal husbandry, fertilization of agricultural fields and human medicine release high amounts these compounds into the environment. The work in this thesis contributes to our understanding of how the selection of bacterial antibiotic resistance can be facilitated by the pollution by metals and antimicrobials. We show that low levels of antibiotics, metals and combinations thereof can lead to the selection of chromosomally encoded antibiotic resistance genes as well as a multidrug resistance plasmid. The underlying genetic and cellular mechanisms of selection identified relate to mutational changes in a plasmid-encoded metal resistance operon, and metal-associated increases in cellular membrane permeability. We further show that exposure to quaternary ammonium compounds can result in cross-resistance to antibiotics following genetic changes in genes related to efflux, membrane synthesis and transcription/translation. Taken together, the work in this thesis suggests that the stewardship of antibiotics should include prudent use of metals and antimicrobials. 

    List of papers
    1. Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals
    Open this publication in new window or tab >>Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals
    Show others...
    2014 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 5, no 5, p. e01918-14-Article in journal (Refereed) Published
    Abstract [en]

    How sublethal levels of antibiotics and heavy metals select for clinically important multidrug resistance plasmids is largely unknown. Carriage of plasmids generally confers substantial fitness costs, implying that for the plasmid-carrying bacteria to be maintained in the population, the plasmid cost needs to be balanced by a selective pressure conferred by, for example, antibiotics or heavy metals. We studied the effects of low levels of antibiotics and heavy metals on the selective maintenance of a 220-kbp extended-spectrum β-lactamase (ESBL) plasmid identified in a hospital outbreak of Klebsiella pneumoniae and Escherichia coli. The concentrations of antibiotics and heavy metals required to maintain plasmid-carrying bacteria, the minimal selective concentrations (MSCs), were in all cases below (almost up to 140-fold) the MIC of the plasmid-free susceptible bacteria. This finding indicates that the very low antibiotic and heavy metal levels found in polluted environments and in treated humans and animals might be sufficiently high to maintain multiresistance plasmids. When resistance genes were moved from the plasmid to the chromosome, the MSC decreased, showing that MSC for a specific resistance conditionally depends on genetic context. This finding suggests that a cost-free resistance could be maintained in a population by an infinitesimally low concentration of antibiotic. By studying the effect of combinations of several compounds, it was observed that for certain combinations of drugs each new compound added lowered the minimal selective concentration of the others. This combination effect could be a significant factor in the selection of multidrug resistance plasmids/bacterial clones in complex multidrug environments.

    IMPORTANCE: Antibiotic resistance is in many pathogenic bacteria caused by genes that are carried on large conjugative plasmids. These plasmids typically contain multiple antibiotic resistance genes as well as genes that confer resistance to biocides and heavy metals. In this report, we show that very low concentrations of single antibiotics and heavy metals or combinations of compounds can select for a large plasmid that carries resistance to aminoglycosides, β-lactams, tetracycline, macrolides, trimethoprim, sulfonamide, silver, copper, and arsenic. Our findings suggest that the low levels of antibiotics and heavy metals present in polluted external environments and in treated animals and humans could allow for selection and enrichment of bacteria with multiresistance plasmids and thereby contribute to the emergence, maintenance, and transmission of antibiotic-resistant disease-causing bacteria.

    National Category
    Microbiology in the medical area
    Research subject
    Microbiology; Molecular Genetics
    Identifiers
    urn:nbn:se:uu:diva-235222 (URN)10.1128/mBio.01918-14 (DOI)000345459000067 ()25293762 (PubMedID)
    Available from: 2014-10-29 Created: 2014-10-29 Last updated: 2018-08-10Bibliographically approved
    2. Mutation in the Copper-Induced sil Operon Enables High-Level Silver Resistance and Silver Facilitated Co-Selection of Multidrug Resistance Plasmid
    Open this publication in new window or tab >>Mutation in the Copper-Induced sil Operon Enables High-Level Silver Resistance and Silver Facilitated Co-Selection of Multidrug Resistance Plasmid
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Human activities are responsible for an accumulation of metals in health care and agricultural environments, and plasmid-encoded metal tolerance operons enable bacteria to rapidly adapt to metal exposure under such conditions. While the mechanisms of action of many metal resistance systems have been described, there is still limited understanding of their role in co-selection of antibiotic resistance in metal-containing environments. Whether plasmid-encoded metal resistance genes confer significant selective advantages is of interest as it has implications for plasmid enrichment and the spread of plasmid-borne antibiotic resistance genes. To increase our understanding of plasmid-mediated metal resistance, we studied the sil operon and its phenotypes in E. coli during growth in the absence and presence of silver and copper. We found that the sil operon provides resistance to both silver and copper. However, it is induced by copper only, and constitutive expression due to point mutations in the two-component silS gene provides high-level silver resistance. Furthermore, we showed that a high-level silver resistant mutant could be enriched in the presence of silver. This enrichment entailed co-selection of the multidrug resistance plasmid pUUH239.2. Our results show that a copper resistance operon can provide high-level silver resistance following a single point mutation, and that the silver resistance phenotype subsequently can co-select for antibiotic resistance in the presence of silver. 

    National Category
    Other Medical Sciences not elsewhere specified
    Identifiers
    urn:nbn:se:uu:diva-356961 (URN)
    Available from: 2018-08-09 Created: 2018-08-09 Last updated: 2018-08-10
    3. Potentiation of the Selective Effect of Antibiotics by Metal Ions
    Open this publication in new window or tab >>Potentiation of the Selective Effect of Antibiotics by Metal Ions
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Complex mixtures of antibiotics and metals are present in many environments ranging from municipal sewage to irrigation water and manure used as agricultural fertilizer. Such mixtures of drugs and metals exert unique selection pressures on local bacterial communities and could function as hotspots for enrichment of antibiotic resistance genes. The presence of metals in the environment has previously been linked to increases in tolerance to antibiotics. In this study, we investigated metal-potentiated selection of antibiotic resistant Salmonella enterica strains. Six environmentally relevant metals were examined in combinations with three different antibiotics. By performing competitions between an antibiotic resistant mutant and the isogenic wild type in each metal-antibiotic combination, we assessed the minimal selective concentration (MSC) of the antibiotic for the resistant strain. The metals silver, cadmium and mercury all exhibited potentiating effects, reducing the MSC of the antibiotic up to 5-fold as compared to in the absence of the metal. We further show that the potentiating metals increased permeability of the cellular outer membrane. These results demonstrate that the presence of a metal can decrease the concentration of an antibiotic required to select for an antibiotic resistant strain, and they indicate that this process involves metal-facilitated uptake of the antibiotic following damage to the outer membrane.

    Keywords
    Antibiotic resistance, Selection
    National Category
    Other Medical Sciences not elsewhere specified
    Identifiers
    urn:nbn:se:uu:diva-356966 (URN)
    Available from: 2018-08-09 Created: 2018-08-09 Last updated: 2018-08-10
    4. Cross-Resistance to Antibiotics After Exposure to Qaternary Ammonium Compounds
    Open this publication in new window or tab >>Cross-Resistance to Antibiotics After Exposure to Qaternary Ammonium Compounds
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Quaternary ammonium compounds (QACs) are common antimicrobials that are used in a variety of consumer products, such as lotions, sunscreen, hair conditioners and hand sanitizers, to inhibit bacterial growth. However, it has been noted that bacteria exposed to QACs can develop resistance, and additionally, resistance to QACs has been observed to provide cross-resistance to antibiotics. In order to identify genetic adaptations for this resistance pattern, we exposed E. coli to three different QACs at sub-MIC and above-MIC concentrations, and identified genetic changes by whole genome sequencing. We found that initial adaptation, at sub-MIC levels, happened through efflux mechanisms, and that subsequent genetic changes, during above-MIC exposure, involved genes associated with the cell membranes and with transcription/translation. We also found that these genetic changes provided cross-resistance to other QACs as well as to several antibiotics.

    Keywords
    Antibiotic resistance, Antimicrobials, Cross-resistance
    National Category
    Other Medical Sciences not elsewhere specified
    Identifiers
    urn:nbn:se:uu:diva-356967 (URN)
    Available from: 2018-08-09 Created: 2018-08-09 Last updated: 2018-08-10
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  • 40.
    Alexander, Michelle
    et al.
    Univ York, York YO10 5DD, N Yorkshire, England.;Univ Aberdeen, Sch Geosci, Dept Archaeol, Aberdeen AB24 3UF, Scotland..
    Ho, Simon Y. W.
    Univ Sydney, Sch Biol Sci, Sydney, NSW 2006, Australia..
    Molak, Martyna
    Polish Acad Sci, Museum & Inst Zool, PL-00679 Warsaw, Poland..
    Barnett, Ross
    Palaeogen & Bioarchaeol Res Network, Res Lab Archaeol, Oxford OX1 3QY, England..
    Carlborg, Örjan
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Dorshorst, Ben
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA..
    Honaker, Christa
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA..
    Besnier, Francois
    Inst Marine Res, Sect Populat Genet, N-5024 Bergen, Norway..
    Wahlberg, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
    Dobney, Keith
    Univ Aberdeen, Sch Geosci, Dept Archaeol, Aberdeen AB24 3UF, Scotland..
    Siegel, Paul
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA..
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden..
    Larson, Greger
    Palaeogen & Bioarchaeol Res Network, Res Lab Archaeol, Oxford OX1 3QY, England..
    Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance2015In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 11, no 10, article id 20150561Article in journal (Refereed)
    Abstract [en]

    Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 x 10(-7) mutations/site/year (95% confidence interval 3.75 x 10(-8)-1.12 x 10(-6)). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.

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  • 41. Alfoeldi, Jessica
    et al.
    Di Palma, Federica
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Williams, Christina
    Kong, Lesheng
    Mauceli, Evan
    Russell, Pamela
    Lowe, Craig B.
    Glor, Richard E.
    Jaffe, Jacob D.
    Ray, David A.
    Boissinot, Stephane
    Shedlock, Andrew M.
    Botka, Christopher
    Castoe, Todd A.
    Colbourne, John K.
    Fujita, Matthew K.
    Moreno, Ricardo Godinez
    ten Hallers, Boudewijn F.
    Haussler, David
    Heger, Andreas
    Heiman, David
    Janes, Daniel E.
    Johnson, Jeremy
    de Jong, Pieter J.
    Koriabine, Maxim Y.
    Lara, Marcia
    Novick, Peter A.
    Organ, Chris L.
    Peach, Sally E.
    Poe, Steven
    Pollock, David D.
    de Queiroz, Kevin
    Sanger, Thomas
    Searle, Steve
    Smith, Jeremy D.
    Smith, Zachary
    Swofford, Ross
    Turner-Maier, Jason
    Wade, Juli
    Young, Sarah
    Zadissa, Amonida
    Edwards, Scott V.
    Glenn, Travis C.
    Schneider, Christopher J.
    Losos, Jonathan B.
    Lander, Eric S.
    Breen, Matthew
    Ponting, Chris P.
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The genome of the green anole lizard and a comparative analysis with birds and mammals2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 477, no 7366, p. 587-591Article in journal (Refereed)
    Abstract [en]

    The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

  • 42. Alho, J. S.
    et al.
    Herczeg, G.
    Laugen, A. T.
    Raesaenen, K.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Merila, J.
    Allen's rule revisited: quantitative genetics of extremity length in the common frog along a latitudinal gradient2011In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 24, no 1, p. 59-70Article in journal (Refereed)
    Abstract [en]

    Ecogeographical rules linking climate to morphology have gained renewed interest because of climate change. Yet few studies have evaluated to what extent geographical trends ascribed to these rules have a genetic, rather than environmentally determined, basis. This applies especially to Allen's rule, which states that the relative extremity length decreases with increasing latitude. We studied leg length in the common frog (Rana temporaria) along a 1500 km latitudinal gradient utilizing wild and common garden data. In the wild, the body size-corrected femur and tibia lengths did not conform to Allen's rule but peaked at mid-latitudes. However, the ratio of femur to tibia length increased in the north, and the common garden data revealed a genetic cline consistent with Allen's rule in some trait and treatment combinations. While selection may have shortened the leg length in the north, the genetic trend seems to be partially masked by environmental effects.

  • 43.
    Ali, Raja Hashim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bogusz, Marcin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A graph-based approach for improving the homologyinference in multiple sequence alignmentsManuscript (preprint) (Other academic)
    Abstract [en]

    Multiple sequence alignment (MSA) is ubiquitous in evolutionary studies and other areas ofbioinformatics. In nearly all cases MSAs are taken to be a known and xed quantity on which toperform downstream analysis despite extensive evidence that MSA accuracy and uncertainty aectsresults. Mistakes in the MSA are known to cause a wide range of problems for downstream evolutionaryinference, ranging from false inference of positive selection to long branch attraction artifacts. The mostpopular approach to dealing with this problem is to remove (lter) specic columns in the MSA thatare thought to be prone to error, either through proximity to gaps or through some scoring function.Although popular, this approach has had mixed success and several studies have even suggested thatltering might be detrimental to phylogenetic studies. Here we present a dierent approach to dealingwith MSA accuracy and uncertainty through a graph-based approach implemented in the freely availablesoftware Divvier. The aim of Divvier is to identify clusters of characters that have strong statisticalevidence of shared homology, based on the output of a pair hidden Markov model. These clusters canthen be used to either lter characters out the MSA, through a process we call partial ltering, or torepresent each of the clusters in a new column, through a process we call divvying up. We validateour approach through its performance on real and simulated benchmarks, nding Divvier substantiallyoutperforms all other ltering software for treating MSAs by retaining more true positive homology callsand removing more false positive homology calls. We also nd that Divvier, in contrast to other lteringtools, can alleviate long branch attraction artifacts induced by MSA and reduces the variation in treeestimates caused by MSA uncertainty.

  • 44.
    Ali, Raja Hashim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ghulam Ishaq Khan Inst Engn Sci & Technol, Fac Comp Sci & Engn, Topi, Pakistan.
    Bogusz, Marcin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments2019In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 10, p. 2340-2351Article in journal (Refereed)
    Abstract [en]

    Multiple sequence alignment (MSA) is ubiquitous in evolution and bioinformatics. MSAs are usually taken to be a known and fixed quantity on which to perform downstream analysis despite extensive evidence that MSA accuracy and uncertainty affect results. These errors are known to cause a wide range of problems for downstream evolutionary inference, ranging from false inference of positive selection to long branch attraction artifacts. The most popular approach to dealing with this problem is to remove (filter) specific columns in the MSA that are thought to be prone to error. Although popular, this approach has had mixed success and several studies have even suggested that filtering might be detrimental to phylogenetic studies. We present a graph-based clustering method to address MSA uncertainty and error in the software Divvier (available at https://github.com/simonwhelan/Divvier), which uses a probabilistic model to identify clusters of characters that have strong statistical evidence of shared homology. These clusters can then be used to either filter characters from the MSA (partial filtering) or represent each of the clusters in a new column (divvying). We validate Divvier through its performance on real and simulated benchmarks, finding Divvier substantially outperforms existing filtering software by retaining more true pairwise homologies calls and removing more false positive pairwise homologies. We also find that Divvier, in contrast to other filtering tools, can alleviate long branch attraction artifacts induced by MSA and reduces the variation in tree estimates caused by MSA uncertainty.

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  • 45.
    Almeida, Pedro
    et al.
    UCL, Dept Genet Evolut & Environm, London, England.
    Proux-Wera, Estelle
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Stockholm, Sweden.
    Churcher, Allison
    Umeå Univ, Dept Mol Biol, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Umeå, Sweden.
    Soler, Lucile
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Dainat, Jacques
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pucholt, Pascal
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology. Swedish Univ Agr Sci, Uppsala BioCtr, Linnean Ctr Plant Biol, Dept Plant Biol, Uppsala, Sweden.
    Nordlund, Jessica
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Martin, Tom
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rönnberg-Wästljung, Ann-Christin
    Swedish Univ Agr Sci, Uppsala BioCtr, Linnean Ctr Plant Biol, Dept Plant Biol, Uppsala, Sweden.
    Nystedt, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Berlin, Sofia
    Swedish Univ Agr Sci, Uppsala BioCtr, Linnean Ctr Plant Biol, Dept Plant Biol, Uppsala, Sweden.
    Mank, Judith E.
    UCL, Dept Genet Evolut & Environm, London, England; Univ British Columbia, Dept Zool, Vancouver, BC, Canada; Univ British Columbia, Biodivers Res Ctr, Vancouver, BC, Canada.
    Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion2020In: BMC Biology, E-ISSN 1741-7007, Vol. 18, no 1, article id 78Article in journal (Refereed)
    Abstract [en]

    Background

    Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.

    Results

    Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.

    Conclusions

    Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.

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  • 46. Alström, Per
    et al.
    Cibois, Alice
    Fjeldså, Jon
    Fuchs, Jerome
    The worldwide expansion of ‘higher’ passerines, and some ancient, relictual lineages2020In: The Largest Avian Radiation: The Evolution of Perching Birds, or the Order Passeriformes / [ed] Fjeldså, J., Christidis, L., Ericson, P.G.P., Barcelona: Lynx Edicions , 2020Chapter in book (Other academic)
  • 47.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    de Juana, Eduardo
    Donald, Paul F.
    Suárez, Francisco
    Mediterranean Short-toed Lark (Alaudala rufescens)2023Other (Other academic)
  • 48.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Donald, Paul F.
    Sharpe's Lark (Mirafra sharpii)2022Other (Other academic)
  • 49.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Donald, Paul F.
    Turkestan Short-toed Lark (Alaudala heinei)2023Other (Other academic)
  • 50.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 , China.
    Mohammadi, Zeinolabedin
    Donald, Paul F
    Nymark, Marianne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Enbody, Erik D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Department of Biomolecular Engineering, University of California, Santa Cruz , Santa Cruz, CA 95060 , USA.
    Irestedt, Martin
    Elisha, Emmanuel Barde
    Ndithia, Henry K
    Tieleman, B Irene
    Engelbrecht, Derek
    Olsson, Urban
    Rancilhac, Loïs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Stervander, Martin
    Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)2023In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642Article in journal (Refereed)
    Abstract [en]

    The species complex comprising the rufous-naped lark Corypha africana, Sharpe’s lark Corypha sharpii, the red-winged lark Corypha hypermetra, the Somali long-billed lark Corypha somalica and Ash’s lark Corypha ashi encompasses 31 recognised taxa across sub-Saharan Africa, many of which are extremely poorly known and some not observed for decades. Only 17 taxa have been studied molecularly and none comprehensively for morphology, vocalisations or other behaviours. Here, we undertake comprehensive integrative taxonomic analyses based on plumage and morphometrics (for 97% of the taxa), mitochondrial and nuclear loci (77%), ≤ 1.3 million genome-wide single nucleotide polymorphisms (68%), song (many described for the first time; 52%) and additional behavioural data (45%). All polytypic species as presently circumscribed are paraphyletic, with eight primary clades separated by ≤ 6.3–6.8 Myr, broadly supported by plumage, morphometrics, song and other behaviours. The most recent divergences concern sympatric taxon pairs usually treated as separate species, whereas the divergence of all clades including C. africana subspecies is as old as sister species pairs in other lark genera. We propose the recognition of nine instead of five species, while C. ashi is synonymised with C. somalica rochei as C. s. ashi. The geographical distributions are incompletely known, and although the nine species are generally para-/allopatric, some might be sympatric.

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    fulltext
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