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  • 1.
    Abbott, Jessica K.
    et al.
    Queen's University.
    Bensch, S.
    Lund University.
    Gosden, Thomas P.
    Lund University.
    Svensson, Erik I.
    Lund University.
    Patterns of differentiation in a colour polymorphism and in neutral markers reveal rapid genetic changes in natural damselfly populations2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 6, p. 1597-1604Article in journal (Refereed)
    Abstract [en]

    The existence and mode of selection operating on heritable adaptive traits can be inferred by comparing population differentiation in neutral genetic variation between populations (often using F(ST) values) with the corresponding estimates for adaptive traits. Such comparisons indicate if selection acts in a diversifying way between populations, in which case differentiation in selected traits is expected to exceed differentiation in neutral markers [F(ST )(selected) > F(ST )(neutral)], or if negative frequency-dependent selection maintains genetic polymorphisms and pulls populations towards a common stable equilibrium [F(ST) (selected) < F(ST) (neutral)]. Here, we compared F(ST) values for putatively neutral data (obtained using amplified fragment length polymorphism) with estimates of differentiation in morph frequencies in the colour-polymorphic damselfly Ischnura elegans. We found that in the first year (2000), population differentiation in morph frequencies was significantly greater than differentiation in neutral loci, while in 2002 (only 2 years and 2 generations later), population differentiation in morph frequencies had decreased to a level significantly lower than differentiation in neutral loci. Genetic drift as an explanation for population differentiation in morph frequencies could thus be rejected in both years. These results indicate that the type and/or strength of selection on morph frequencies in this system can change substantially between years. We suggest that an approach to a common equilibrium morph frequency across all populations, driven by negative frequency-dependent selection, is the cause of these temporal changes. We conclude that inferences about selection obtained by comparing F(ST) values from neutral and adaptive genetic variation are most useful when spatial and temporal data are available from several populations and time points and when such information is combined with other ecological sources of data.

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  • 2.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA.
    Bonnedahl, Jonas
    Linkoping Univ, Dept Clin & Expt Med, Linkoping, Sweden;Kalmar Cty Council, Dept Infect Dis, Kalmar, Sweden.
    Woksepp, Hanna
    Kalmar Cty Hosp, Res Sect, Dept Dev & Publ Hlth, Kalmar, Sweden.
    Hernandez, Jorge
    Kalmar Cty Hosp, Dept Clin Microbiol, Kalmar, Sweden.
    Reed, John A.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA.
    Tibbitts, Lee
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA.
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    Douglas, David C.
    US Geol Survey, Alaska Sci Ctr, Juneau, AK USA.
    Ramey, Andrew M.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA.
    Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial-resistant Escherichia coli on the Kenai Peninsula, Alaska2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 10, p. 2531-2545Article in journal (Refereed)
    Abstract [en]

    Gulls (Larus spp.) have frequently been reported to carry Escherichia coli exhibiting antimicrobial resistance (AMR E. coli); however, the pathways governing the acquisition and dispersal of such bacteria are not well described. We equipped 17 landfill-foraging gulls with satellite transmitters and collected gull faecal samples longitudinally from four locations on the Kenai Peninsula, Alaska to assess: (a) gull attendance and transitions between sites, (b) spatiotemporal prevalence of faecally shed AMR E. coli, and (c) genomic relatedness of AMR E. coli isolates among sites. We also sampled Pacific salmon (Oncorhynchus spp.) harvested as part of personal-use dipnet fisheries at two sites to assess potential contamination with AMR E. coli. Among our study sites, marked gulls most commonly occupied the lower Kenai River (61% of site locations) followed by the Soldotna landfill (11%), lower Kasilof River (5%) and upper Kenai River (<1%). Gulls primarily moved between the Soldotna landfill and the lower Kenai River (94% of transitions among sites), which were also the two locations with the highest prevalence of AMR E. coli. There was relatively high spatial and temporal variability in AMR E. coli prevalence in gull faeces and there was no evidence of contamination on salmon harvested in personal-use fisheries. We identified E. coli sequence types and AMR genes of clinical importance, with some isolates possessing genes associated with resistance to as many as eight antibiotic classes. Our findings suggest that gulls acquire AMR E. coli at habitats with anthropogenic inputs and subsequent movements may represent pathways through which AMR is dispersed.

  • 3.
    Ament-Velasquez, Sandra Lorena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Figuet, E.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Ballenghien, M.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Zattara, E. E.
    Indiana Univ, Dept Biol, 107 S Indiana Ave, Bloomington, IN 47405 USA.;Smithsonian Inst, Natl Museum Nat Hist, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA..
    Norenburg, J. L.
    Smithsonian Inst, Natl Museum Nat Hist, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA..
    Fernandez-Alvarez, F. A.
    CSIC Barcelona, Inst Ciencies Mar, Barcelona 08003, Spain..
    Bierne, J.
    Univ Reims, Lab Biol Cellulaire & Mol, 9 Blvd Paix, F-51100 Reims, France..
    Bierne, N.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Galtier, N.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 14, p. 3356-3369Article in journal (Refereed)
    Abstract [en]

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

  • 4. Antoniazza, Sylvain
    et al.
    Kanitz, Ricardo
    Neuenschwander, Samuel
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gaigher, Arnaud
    Roulin, Alexandre
    Goudet, Jerome
    Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 22, p. 5508-5523Article, review/survey (Refereed)
    Abstract [en]

    Gradients of variationor clineshave always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait. A third neutral process, surfing of a newly arisen mutation during the colonization of a new habitat, is more difficult to test. Here, we designed a spatially explicit approximate Bayesian computation (ABC) simulation framework to evaluate whether the strong cline in the genetically based reddish coloration observed in the European barn owl (Tyto alba) arose as a by-product of a range expansion or whether selection has to be invoked to explain this colour cline, for which we have previously ruled out the actions of IBD or secondary contact. Using ABC simulations and genetic data on 390 individuals from 20 locations genotyped at 22 microsatellites loci, we first determined how barn owls colonized Europe after the last glaciation. Using these results in new simulations on the evolution of the colour phenotype, and assuming various genetic architectures for the colour trait, we demonstrate that the observed colour cline cannot be due to the surfing of a neutral mutation. Taking advantage of spatially explicit ABC, which proved to be a powerful method to disentangle the respective roles of selection and drift in range expansions, we conclude that the formation of the colour cline observed in the barn owl must be due to natural selection.

  • 5.
    Arnqvist, Göran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rowe, Locke
    Uppsala University, Swedish Collegium for Advanced Study (SCAS). Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada.
    Ecology, the pace‐of‐life, epistatic selection and the maintenance of genetic variation in life‐history genes2023In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 17, p. 4713-4724Article in journal (Refereed)
    Abstract [en]

    Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.

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  • 6.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hultin-Rosenberg, Lina
    Brandström, Mikael
    Zwalen, Martin
    Clayton, David F.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Natural selection in protein-coding genes expressed in avian brain2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 12, p. 3008-3017Article in journal (Refereed)
    Abstract [en]

    The evolution of birds from theropod dinosaurs took place approximately 150 million years ago, and was associated with a number of specific adaptations that are still evident among extant birds, including feathers, song and extravagant secondary sexual characteristics. Knowledge about the molecular evolutionary background to such adaptations is lacking. Here, we analyse the evolution of > 5000 protein-coding gene sequences expressed in zebra finch brain by comparison to orthologous sequences in chicken. Mean d(N)/d(S) is 0.085 and genes with their maximal expression in the eye and central nervous system have the lowest mean d(N)/d(S) value, while those expressed in digestive and reproductive tissues exhibit the highest. We find that fast-evolving genes (those which have higher than expected rate of nonsynonymous substitution, indicative of adaptive evolution) are enriched for biological functions such as fertilization, muscle contraction, defence response, response to stress, wounding and endogenous stimulus, and cell death. After alignment to mammalian orthologues, we identify a catalogue of 228 genes that show a significantly higher rate of protein evolution in the two bird lineages than in mammals. These accelerated bird genes, representing candidates for avian-specific adaptations, include genes implicated in vocal learning and other cognitive processes. Moreover, colouration genes evolve faster in birds than in mammals, which may have been driven by sexual selection for extravagant plumage characteristics.

  • 7.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Fagerberg, Sofie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 4, p. 964-980Article in journal (Refereed)
    Abstract [en]

    Although there is growing interest to take genomics into the complex realms of natural populations, there is a general shortage of genomic resources and tools available for wild species. This applies not at least to birds, for which genomic approaches should be helpful to questions such as adaptation, speciation and population genetics. In this study, we describe a genome-wide reference set of conserved avian gene markers, broadly applicable across birds. By aligning protein-coding sequences from the recently assembled chicken genome with orthologous sequences in zebra finch, we identified particularly conserved exonic regions flanking introns of suitable size for subsequent amplification and sequencing. Primers were designed for 242 gene markers evenly distributed across the chicken genome, with a mean inter-marker interval of 4.2 Mb. Between 78% and 93% of the markers amplified a specific product in five species tested (chicken, peregrine falcon, collared flycatcher, great reed warbler and blue tit). Two hundred markers were sequenced in collared flycatcher, yielding a total of 122.41 kb of genomic DNA sequence (12096 bp coding sequence and 110 314 bp noncoding). Intron size of collared flycatcher and chicken was highly correlated, as was GC content. A polymorphism screening using these markers in a panel of 10 unrelated collared flycatchers identified 871 single nucleotide polymorphisms (pi = 0.0029) and 33 indels (mainly very short). Avian genome characteristics such as uniform genome size and low rate of syntenic rearrangements suggest that this marker set will find broad utility as a genome-wide reference resource for molecular ecological and population genomic analysis of birds. We envision that it will be particularly useful for obtaining large-scale orthologous targets in different species--important in, for instance, phylogenetics--and for large-scale identification of evenly distributed single nucleotide polymorphisms needed in linkage mapping or in studies of gene flow and hybridization.

  • 8.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Palkopoulou, Eleftheria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 16, p. 3394-3405Article in journal (Refereed)
    Abstract [en]

    Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridization, these two species demonstrate a high degree of intrinsic post-zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-chromosome. Could rearrangements of the Z-chromosome between the species explain their reproductive isolation? We developed high coverage Z-chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57-62 gene markers with an estimated average density of one every 1-1.5 Mb. We estimated the recombination rates in flycatcher Z-chromosomes to 1.1-1.3 cM/Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex chromosome rearrangements have caused the relatively strong post-zygotic reproductive isolation between these two Ficedula species.

  • 9. Beaumont, Mark A
    et al.
    Nielsen, Rasmus
    Robert, Christian
    Hey, Jody
    Gaggiotti, Oscar
    Knowles, Lacey
    Estoup, Arnaud
    Panchal, Mahesh
    Corander, Jukka
    Hickerson, Mike
    Sisson, Scott A
    Fagundes, Nelson
    Chikhi, Lounès
    Beerli, Peter
    Vitalis, Renaud
    Cornuet, Jean-Marie
    Huelsenbeck, John
    Foll, Matthieu
    Yang, Ziheng
    Rousset, Francois
    Balding, David
    Excoffier, Laurent
    In defence of model-based inference in phylogeography.2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 3, p. 436-446Article in journal (Refereed)
    Abstract [en]

    Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.

  • 10.
    Beier, Sara
    et al.
    Leibniz Inst Baltic Sea Res Warnemunde IOW, Biol Oceanog, Rostock, Germany.;Sorbonne Univ, Observ Oceanol Banyuls, Lab Oceanog Microbienne LOMIC, CNRS, Banyuls Sur Mer, France..
    Andersson, Anders F.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden..
    Galand, Pierre E.
    Sorbonne Univ, Observ Oceanol Banyuls, Lab Ecogeochim Environm Benth LECOB, CNRS, Banyuls Sur Mer, France..
    Hochart, Corentin
    Sorbonne Univ, Observ Oceanol Banyuls, Lab Ecogeochim Environm Benth LECOB, CNRS, Banyuls Sur Mer, France..
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    McMahon, Katherine
    Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA.;Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA..
    Bertilsson, Stefan
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden..
    The environment drives microbial trait variability in aquatic habitats2020In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 29, no 23, p. 4605-4617Article in journal (Refereed)
    Abstract [en]

    A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.

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  • 11.
    Berdan, Emma L.
    et al.
    Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Blanckaert, Alexandre
    Univ Wisconsin, Lab Genet, Madison, WI 53706 USA..
    Slotte, Tanja
    Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Suh, Alexander
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ East Anglia, Sch Biol Sci Organisms & Environm, Norwich, Norfolk, England..
    Westram, Anja M.
    IST Austria, Klosterneuburg, Austria.;Nord Univ, Fac Biosci & Aquaculture, Bodo, Norway..
    Fragata, Ines
    Univ Lisbon, Fac Ciencias, cE3c Ctr Ecol Evolut & Environm Changes, Lisbon, Portugal..
    Unboxing mutations: Connecting mutation types with evolutionary consequences2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 12, p. 2710-2723Article in journal (Refereed)
    Abstract [en]

    A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.

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    fulltext
  • 12.
    Berglund, Eva C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Ellegaard, Kirsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Granberg, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Xie, Zhoupeng
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Maruyama, Soichi
    Kosoy, Michael Y.
    Birtles, Richard J.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Rapid diversification by recombination in Bartonella grahamii from wild rodents in Asia contrasts with low levels of genomic divergence in Northern Europe and America2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 11, p. 2241-2255Article in journal (Refereed)
    Abstract [en]

    Bartonella is a genus of vector-borne bacteria that infect the red blood cells of mammals, and includes several human-specific and zoonotic pathogens. Bartonella grahamii has a wide host range and is one of the most prevalent Bartonella species in wild rodents. We studied the population structure, genome content and genome plasticity of a collection of 26 B. grahamii isolates from 11 species of wild rodents in seven countries. We found strong geographic patterns, high recombination frequencies and large variations in genome size in B. grahamii compared with previously analysed cat- and human-associated Bartonella species. The extent of sequence divergence in B. grahamii populations was markedly lower in Europe and North America than in Asia, and several recombination events were predicted between the Asian strains. We discuss environmental and demographic factors that may underlie the observed differences.

  • 13.
    Björklund, Mats
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Spong, Göran
    Johansson, Malin
    High genetic variation in leopards indicates large and long-term stable effective population size2000In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 9, p. 1773-1782Article in journal (Refereed)
  • 14.
    Boman, Jesper
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zhu, Yishu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höök, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vila, Roger
    Univ Pompeu Fabra, Inst Biol Evolut, CSIC, Barcelona, Spain.
    Talavera, Gerard
    CSIC Ajuntament Barcelona, Inst Bot Barcelona IBB, Barcelona, Spain.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui)2023In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 13, p. 3513-3523Article in journal (Refereed)
    Abstract [en]

    Seasonal environmental fluctuations provide formidable challenges for living organisms, especially small ectotherms such as butterflies. A common strategy to cope with harsh environments is to enter diapause, but some species avoid unsuitable conditions by migrating. Despite a growing understanding of migration in the life cycles of some butterfly species, it remains unknown how individuals register and store environmental cues to determine whether and where to migrate. Here, we explored how competition and host plant availability during larval development affect patterns of DNA methylation in the migratory painted lady (Vanessa cardui) butterfly. We identify a set of potentially functional methylome shifts associated with differences in the environment, indicating that DNA methylation is involved in the response to different conditions during larval development. By analysing the transcriptome for the same samples used for methylation profiling, we also uncovered a non-monotonic relationship between gene body methylation and gene expression. Our results provide a starting point for understanding the interplay between DNA methylation and gene expression in butterflies in general and how differences in environmental conditions during development can trigger unique epigenetic marks that might be important for behavioural decisions in the adult stage.

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  • 15. Brace, Selina
    et al.
    Barnes, Ian
    Powell, Adam
    Pearson, Rebecca
    Woolaver, Lance G.
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Turvey, Samuel T.
    Population history of the Hispaniolan hutia Plagiodontia aedium (Rodentia Capromyidae): testing the model of ancient differentiation on a geotectonically complex Caribbean island2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 9, p. 2239-2253Article in journal (Refereed)
    Abstract [en]

    Hispaniola is a geotectonically complex island consisting of two palaeo-islands that docked c. 10 Ma, with a further geological boundary subdividing the southern palaeo-island into eastern and western regions. All three regions have been isolated by marine barriers during the late Cenozoic and possess biogeographically distinct terrestrial biotas. However, there is currently little evidence to indicate whether Hispaniolan mammals show distributional patterns reflecting this geotectonic history, as the islands endemic land mammal fauna is now almost entirely extinct. We obtained samples of Hispaniolan hutia (Plagiodontia aedium), one of the two surviving Hispaniolan land mammal species, through fieldwork and historical museum collections from seven localities distributed across all three of the islands biogeographic regions. Phylogenetic analysis using mitochondrial DNA (cytochrome b) reveals a pattern of historical allopatric lineage divergence in this species, with the spatial distribution of three distinct hutia lineages biogeographically consistent with the islands geotectonic history. Coalescent modelling, approximate Bayesian computation and approximate Bayes factor analyses support our phylogenetic inferences, indicating near-complete genetic isolation of these biogeographically separate populations and differing estimates of their effective population sizes. Spatial congruence of hutia lineage divergence is not however matched by temporal congruence with divergences in other Hispaniolan taxa or major events in Hispaniolas geotectonic history; divergence between northern and southern hutia lineages dates to c. 0.6 Ma, significantly later than the unification of the palaeo-islands. The three allopatric Plagiodontia populations should all be treated as distinct management units for conservation, with particular attention required for the northern population (low haplotype diversity) and the south-western population (high haplotype diversity but highly threatened).

  • 16.
    Breed, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Marklund, Maria H. K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ottewell, Kym M.
    Gardner, Michael G.
    Harris, J. Berton C.
    Lowe, Andrew J.
    Pollen diversity matters: revealing the neglected effect of pollen diversity on fitness in fragmented landscapes2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 24, p. 5955-5968Article in journal (Refereed)
    Abstract [en]

    Few studies have documented the impacts of habitat fragmentation on plant mating patterns together with fitness. Yet, these processes require urgent attention to better understand the impact of contemporary landscape change on biodiversity and for guiding native plant genetic resource management. We examined these relationships using the predominantly insect-pollinated Eucalyptus socialis. Progeny were collected from trees located in three increasingly disturbed landscapes in southern Australia and were planted out in common garden experiments. We show that individual mating patterns were increasingly impacted by lower conspecific density caused by habitat fragmentation. We determined that reduced pollen diversity probably has effects over and above those of inbreeding on progeny fitness. This provides an alternative mechanistic explanation for the indirect density dependence often inferred between conspecific density and offspring fitness.

  • 17.
    Burley, John T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA; Brown Univ, Dept Ecol Evolut & Organismal Biol, Providence, RI USA; Brown Univ, Inst Brown Environm & Soc, Providence, RI USA.
    Orzechowski, Sophia C. M.
    Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA..
    Sin, Simon Yung Wa
    Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA.;Univ Hong Kong, Sch Biol Sci, Hong Kong, Peoples R China..
    Edwards, Scott V.
    Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA..
    Whole-genome phylogeography of the blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome2023In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 6, p. 1248-1270Article in journal (Refereed)
    Abstract [en]

    Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3–1.7 Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome; and in E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination-suppressed portion of the neo-Z (~37.2 Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral-Z. Yet, the new PAR (~17.4 Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.

  • 18. Campos, Paula F.
    et al.
    Kristensen, Tommy
    Orlando, Ludovic
    Sher, Andrei
    Kholodova, Marina V.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hofreiter, Michael
    Drucker, Dorothee G.
    Kosintsev, Pavel
    Tikhonov, Alexei
    Baryshnikov, Gennady F.
    Willerslev, Eske
    Gilbert, M. Thomas P.
    Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 22, p. 4863-4875Article in journal (Refereed)
    Abstract [en]

    Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49 500 C-14 ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40 400 to 10 250 C-14 ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.

  • 19.
    Capador‐Barreto, Hernán D.
    et al.
    Uppsala Biocentre Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden.
    Bernhardsson, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala Biocentre Department of Plant Biology Swedish University of Agricultural Sciences Uppsala Sweden.
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vos, Ingrid
    Forestry Research Institute of Sweden (Skogforsk) Ekebo Sweden.
    Lundén, Karl
    Uppsala Biocentre Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden.
    Wu, Harry X.
    Umeå Plant Science Centre Department of Forest Genetics and Plant Physiology Swedish University of Agricultural Sciences Umeå Sweden.
    Karlsson, Bo
    Forestry Research Institute of Sweden (Skogforsk) Ekebo Sweden.
    Ingvarsson, Pär K.
    Uppsala Biocentre Department of Plant Biology Swedish University of Agricultural Sciences Uppsala Sweden.
    Stenlid, Jan
    Uppsala Biocentre Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden.
    Elfstrand, Malin
    Uppsala Biocentre Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden.
    Killing two enemies with one stone?: Genomics of resistance to two sympatric pathogens in Norway spruce2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 18, p. 4433-4447Article in journal (Refereed)
    Abstract [en]

    Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.

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  • 20.
    Christmas, Matthew J
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bunikis, Ignas
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Olsson, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wallerman, Ola
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Webster, Matthew T
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Chromosomal inversions associated with environmental adaptation in honeybees2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 6, p. 1358-1374Article in journal (Refereed)
    Abstract [en]

    Chromosomal inversions can facilitate local adaptation in the presence of gene flow by suppressing recombination between well-adapted native haplotypes and poorly adapted migrant haplotypes. East African mountain populations of the honeybee Apis mellifera are highly divergent from neighbouring lowland populations at two extended regions in the genome, despite high similarity in the rest of the genome, suggesting that these genomic regions harbour inversions governing local adaptation. Here, we utilize a new highly contiguous assembly of the honeybee genome to characterize these regions. Using whole-genome sequencing data from 55 highland and lowland bees, we find that the highland haplotypes at both regions are present at high frequencies in three independent highland populations but extremely rare elsewhere. The boundaries of both divergent regions are characterized by regions of high homology with each other positioned in opposite orientations and contain highly repetitive, long inverted repeats with homology to transposable elements. These regions are likely to represent inversion breakpoints that participate in nonallelic homologous recombination. Using long-read data, we confirm that the lowland samples are contiguous across breakpoint regions. We do not find evidence for disruption of functional sequence by these breakpoints, which suggests that the inversions are likely maintained due to their allelic content conferring local adaptation in highland environments. Finally, we identify a third divergent genomic region, which contains highly divergent segregating haplotypes that also may contain inversion variants under selection. The results add to a growing body of evidence indicating the importance of chromosomal inversions in local adaptation.

  • 21.
    Christmas, Matthew
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jones, Julia C.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Coll Dublin, Sch Biol & Environm Sci, Dublin, Ireland..
    Olsson, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wallerman, Ola
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Bunikis, Ignas
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Kierczak, Marcin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Whitley, Kaitlyn M.
    Appalachian State Univ, Dept Biol, Boone, NC 28608 USA.;ARS, USDA, Charleston, SC USA..
    Sullivan, Isabel
    Appalachian State Univ, Dept Biol, Boone, NC 28608 USA.;Univ Maryland, Marine Estuarine Environm Sci, College Pk, MD 20742 USA..
    Geib, Jennifer C.
    Appalachian State Univ, Dept Biol, Boone, NC 28608 USA..
    Miller-Struttmann, Nicole E.
    Webster Univ, Biol Sci Dept, St Louis, MO USA..
    Webster, Matthew Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component2022In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 31, no 4, p. 1111-1127Article in journal (Refereed)
    Abstract [en]

    Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.

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  • 22.
    Christmas, Matthew
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jones, Julia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala Univ, Dept Med Biochem & Microbiol, Sci Life Lab, Uppsala, Sweden.;Univ Coll Dublin, Sch Biol & Environm Sci, Dublin, Ireland..
    Olsson, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wallerman, Ola
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Bunikis, Ignas
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Kierczak, Marcin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Whitley, Kaitlyn M.
    Appalachian State Univ, Dept Biol, Boone, NC 28608 USA.;ARS, USDA, Charleston, SC USA..
    Sullivan, Isabel
    Appalachian State Univ, Dept Biol, Boone, NC 28608 USA.;Univ Maryland, Marine Estuarine Environm Sci, College Pk, MD 20742 USA..
    Geib, Jennifer C.
    Appalachian State Univ, Dept Biol, Boone, NC 28608 USA..
    Miller-Struttmann, Nicole E.
    Webster Univ, Biol Sci Dept, St Louis, MO USA..
    Webster, Matthew Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component2022In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 31, no 4, p. 1111-1127Article in journal (Refereed)
    Abstract [en]

    Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.

  • 23.
    Cornille, Amandine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Salcedo, A.
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M6R 1M3, Canada..
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wright, S. I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M6R 1M3, Canada..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 616-629Article in journal (Refereed)
    Abstract [en]

    Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C.bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C.bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C.bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C.bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.

  • 24.
    Craig, Rory J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Edinburgh, Sch Biol Sci, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wang, Mi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 2, p. 476-492Article in journal (Refereed)
    Abstract [en]

    It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence are particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts. We report that similar to 6.6% of the collared flycatcher genome (74.0Mb) is spanned by similar to 1.28 million CEs, a higher proportion of the genome but a lower total amount of conserved sequence than has been reported in mammals. We identified >200,000 CEs specific to either the archosaur, avian, neoavian or passeridan lineages, constituting candidates for lineage-specific adaptations. Importantly, no less than similar to 71% of CE sites were nonexonic (52.6Mb), and conserved nonexonic sequence density was negatively correlated with functional exonic density at local genomic scales. Additionally, nucleotide diversity was strongly reduced at nonexonic conserved sites (0.00153) relative to intergenic nonconserved sites (0.00427). By integrating deep transcriptome sequencing and additional genome annotation, we identified novel protein-coding genes, long noncoding RNA genes and transposon-derived (exapted) CEs. The approach taken here based on the use of a progressive cactus whole-genome alignment to identify CEs should be readily applicable to nonmodel organisms in general and help to reveal the rich repertoire of putatively functional noncoding sequence as targets for selection.

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  • 25.
    Darolti, Iulia
    et al.
    UCL, Dept Genet Evolut & Environm, London, England.
    Wright, Alison E.
    UCL, Dept Genet Evolut & Environm, London, England;Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Pucholt, Pascal
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Dept Plant Biol, Uppsala, Sweden.
    Berlin, Sofia
    Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Dept Plant Biol, Uppsala, Sweden.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London, England.
    Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 3, p. 694-708Article in journal (Refereed)
    Abstract [en]

    The relative rate of evolution for sex-biased genes has often been used as a measure of the strength of sex-specific selection. In contrast to studies in a wide variety of animals, far less is known about the molecular evolution of sex-biased genes in plants, particularly in dioecious angiosperms. Here, we investigate the gene expression patterns and evolution of sex-biased genes in the dioecious plant Salix viminalis. We observe lower rates of sequence evolution for male-biased genes expressed in the reproductive tissue compared to unbiased and female-biased genes. These results could be partially explained by the lower codon usage bias for male-biased genes leading to elevated rates of synonymous substitutions compared to unbiased genes. However, the stronger haploid selection in the reproductive tissue of plants, together with pollen competition, would also lead to higher levels of purifying selection acting to remove deleterious variation. Future work should focus on the differential evolution of haploid- and diploid-specific genes to understand the selective dynamics acting on these loci.

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  • 26.
    Decroocq, Stephane
    et al.
    INRA, UMR BFP 1332, Equipe Virol, 71 Ave Edouard Bourlaux, F-33882 Villenave Dornon, France.;Univ Bordeaux, UMR BFP 1332, CS20032, F-33882 Villenave Dornon, France..
    Cornille, Amandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Science for Life Laboratory, SciLifeLab. Swiss Fed Inst Technol, Ctr Adaptat Changing Environm, CH-8092 Zurich, Switzerland..
    Tricon, David
    INRA, UMR BFP 1332, Equipe Virol, 71 Ave Edouard Bourlaux, F-33882 Villenave Dornon, France.;Univ Bordeaux, UMR BFP 1332, CS20032, F-33882 Villenave Dornon, France..
    Babayeva, Sevda
    ANAS, Genet Resources Inst, Azadlig Ave 155, AZ-1106 Baku, Azerbaijan..
    Chague, Aurelie
    INRA, UMR BFP 1332, Equipe Virol, 71 Ave Edouard Bourlaux, F-33882 Villenave Dornon, France.;Univ Bordeaux, UMR BFP 1332, CS20032, F-33882 Villenave Dornon, France..
    Eyquard, Jean-Philippe
    INRA, UMR BFP 1332, Equipe Virol, 71 Ave Edouard Bourlaux, F-33882 Villenave Dornon, France.;Univ Bordeaux, UMR BFP 1332, CS20032, F-33882 Villenave Dornon, France..
    Karychev, Raul
    Kazakh Res Inst Hort & Viticulture, 238-A Gagarin Ave, Alma Ata 480060, Kazakhstan..
    Dolgikh, Svetlana
    Kazakh Res Inst Hort & Viticulture, 238-A Gagarin Ave, Alma Ata 480060, Kazakhstan..
    Kostritsyna, Tatiana
    Natl Acad Sci, Bot Garden, Akhunbaeva St 1a, Bishkek 720064, Kyrgyzstan.;Int Sch Med, 1 F,St Intergelpo, Bishkek 720054, Kyrgyzstan..
    Liu, Shuo
    INRA, UMR BFP 1332, Equipe Virol, 71 Ave Edouard Bourlaux, F-33882 Villenave Dornon, France.;Univ Bordeaux, UMR BFP 1332, CS20032, F-33882 Villenave Dornon, France.;Liaoning Inst Pomol, Tiedong St, Yingkou City 115009, Liaoning, Peoples R China..
    Liu, Weisheng
    Liaoning Inst Pomol, Tiedong St, Yingkou City 115009, Liaoning, Peoples R China..
    Geng, Wenjuan
    Xinjiang Agr Univ, Coll Hort & Forestry Sci, 311 NongDaDong Rd, Urumqi City 830052, Xinjiang, Peoples R China..
    Liao, Kang
    Xinjiang Agr Univ, Coll Hort & Forestry Sci, 311 NongDaDong Rd, Urumqi City 830052, Xinjiang, Peoples R China..
    Asma, Bayram M.
    Inonu Univ, Dept Hort, TR-44210 Malatya, Turkey..
    Akparov, Zeynal
    ANAS, Genet Resources Inst, Azadlig Ave 155, AZ-1106 Baku, Azerbaijan..
    Giraud, Tatiana
    Univ Paris Saclay, Univ Paris Sud, Ecol Systemat Evolut, CNRS,AgroParisTech, Orsay, France..
    Decroocq, Veronique
    INRA, UMR BFP 1332, Equipe Virol, 71 Ave Edouard Bourlaux, F-33882 Villenave Dornon, France.;Univ Bordeaux, UMR BFP 1332, CS20032, F-33882 Villenave Dornon, France..
    New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 19, p. 4712-4729Article in journal (Refereed)
    Abstract [en]

    Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.

  • 27. Demontis, Ditte
    et al.
    Pertoldi, Cino
    Loeschcke, Volker
    Mikkelsen, Karina
    Axelsson, Tomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Kristensen, Nygaard
    Efficiency of selection, as measured by single nucleotide polymorphism variation, is dependent on inbreeding rate in Drosophila melanogaster2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, no 22, p. 4551-4563Article in journal (Refereed)
    Abstract [en]

    It is often hypothesized that slow inbreeding causes less inbreeding depression than fast inbreeding at the same absolute level of inbreeding. Possible explanations for this phenomenon include the more efficient purging of deleterious alleles and more efficient selection for heterozygote individuals during slow, when compared with fast, inbreeding. We studied the impact of inbreeding rate on the loss of heterozygosity and on morphological traits in Drosophila melanogaster. We analysed five noninbred control lines, 10 fast inbred lines and 10 slow inbred lines; the inbred lines all had an expected inbreeding coefficient of approximately 0.25. Forty single nucleotide polymorphisms in DNA coding regions were genotyped, and we measured the size and shape of wings and counted the number of sternopleural bristles on the genotyped individuals. We found a significantly higher level of genetic variation in the slow inbred lines than in the fast inbred lines. This higher genetic variation was resulting from a large contribution from a few loci and a smaller effect from several loci. We attributed the increased heterozygosity in the slow inbred lines to the favouring of heterozygous individuals over homozygous individuals by natural selection, either by associative over-dominance or balancing selection, or a combination of both. Furthermore, we found a significant polynomial correlation between genetic variance and wing size and shape in the fast inbred lines. This was caused by a greater number of homozygous individuals among the fast inbred lines with small, narrow wings, which indicated inbreeding depression. Our results demonstrated that the same amount of inbreeding can have different effects on genetic variance depending on the inbreeding rate, with slow inbreeding leading to higher genetic variance than fast inbreeding. These results increase our understanding of the genetic basis of the common observation that slow inbred lines express less inbreeding depression than fast inbred lines. In addition, this has more general implications for the importance of selection in maintaining genetic variation.

  • 28. Dittmar, Emily L.
    et al.
    Oakley, Christopher G.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Schemske, Douglas W.
    Flowering time QTL in natural populations of Arabidopsis thaliana and implications for their adaptive value2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 17, p. 4291-4303Article in journal (Refereed)
    Abstract [en]

    The genetic basis of phenotypic traits is of great interest to evolutionary biologists, but their contribution to adaptation in nature is often unknown. To determine the genetic architecture of flowering time in ecologically relevant conditions, we used a recombinant inbred line population created from two locally adapted populations of Arabidopsis thaliana from Sweden and Italy. Using these RILs, we identified flowering time QTL in growth chambers that mimicked the natural temperature and photoperiod variation across the growing season in each native environment. We also compared the genomic locations of flowering time QTL to those of fitness (total fruit number) QTL from a previous three-year field study. Ten total flowering time QTL were found, and in all cases, the Italy genotype caused early flowering regardless of the conditions. Two QTL were consistent across chamber environments, and these had the largest effects on flowering time. Five of the fitness QTL colocalized with flowering time QTL found in the Italy conditions, and in each case, the local genotype was favoured. In contrast, just two flowering time QTL found in the Sweden conditions colocalized with fitness QTL and in only one case was the local genotype favoured. This implies that flowering time may be more important for adaptation in Italy than Sweden. Two candidate genes (FLC and VIN3) underlying the major flowering time QTL found in the current study are implicated in local adaptation.

  • 29.
    Dussex, Nicolas
    et al.
    Univ Otago, Dept Anat, Dunedin, New Zealand.;Swedish Museum Nat Hist, Dept Bioinformat & Genet, Ctr Palaeogenet, Svante Arrhenius Vag 20C, SE-10691 Stockholm, Sweden..
    Kutschera, Verena E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Stockholm Univ, Natl Bioinformat Infrastruct Sweden, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Wiberg, R. Axel W.
    Univ St Andrews, Sch Biol, Ctr Biol Diversity, St Andrews, Fife, Scotland.;Univ Basel, Dept Environm Sci, Evolutionary Biol, Basel, Switzerland..
    Parker, Darren J.
    Univ St Andrews, Sch Biol, Ctr Biol Diversity, St Andrews, Fife, Scotland.;Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland..
    Hunt, Gavin R.
    Univ Auckland, Sci Ctr 302, Auckland, New Zealand..
    Gray, Russell D.
    Univ Auckland, Sci Ctr 302, Auckland, New Zealand.;Max Planck Inst Sci Human Hist, Jena, Germany..
    Rutherford, Kim
    Univ Otago, Dept Anat, Dunedin, New Zealand..
    Abe, Hideaki
    Univ Otago, Dept Anat, Dunedin, New Zealand.;Kyoto Univ, Wildlife Res Ctr, Kyoto, Japan..
    Fleischer, Robert C.
    Smithsonian Conservat Biol Inst, Ctr Conservat Genom, Washington, DC USA..
    Ritchie, Michael G.
    Univ St Andrews, Sch Biol, Ctr Biol Diversity, St Andrews, Fife, Scotland..
    Rutz, Christian
    Univ St Andrews, Sch Biol, Ctr Biol Diversity, St Andrews, Fife, Scotland..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany..
    Gemmell, Neil J.
    Univ Otago, Dept Anat, Dunedin, New Zealand..
    A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 4, p. 973-986Article in journal (Refereed)
    Abstract [en]

    Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.

  • 30.
    Dutoit, Ludovic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bolivar, Paulina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wang, Mi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nadachowska-Brzyska, Krystyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Smeds, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 18, p. 3572-3581Article in journal (Other academic)
    Abstract [en]

    Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on sexually antagonistic mutations in males and females. This prediction, so far not been empirically tested on a genome-wide scale, could potentially contribute towards genomic heterogeneity in levels of genetic diversity. We used large-scale population genomic and transcriptomic data from the collared flycatcher (Ficedula albicollis) to analyse how sex-biased gene expression – one outcome of sexual conflict – relates to genetic variability. Here, we demonstrate that the extent of sex-biased gene expression of both male-biased and female-biased genes is significantly correlated with levels of nucleotide diversity in gene sequences and that this correlation extends to the overall levels of genomic diversity. We find evidence for balancing selection in sex-biased genes, suggesting that sex-biased gene expression could be seen as a component counteracting the diversity-reducing effects of linked positive and purifying selection. The observation of significant genetic differentiation between males and females for male-biased genes indicates ongoing sexual conflict and sex-specific viability selection, potentially driven by sexual selection. Our results thus provide a new perspective on the long-standing question in evolutionary biology of how genomes can remain so genetically variable in face of strong natural and sexual selection.

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  • 31. Edelaar, Pim
    et al.
    Björklund, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    If F-ST does not measure neutral genetic differentiation, then comparing it with Q(ST) is misleading. Or is it?2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 9, p. 1805-1812Article in journal (Refereed)
    Abstract [en]

    The comparison between neutral genetic differentiation (F-ST) and quantitative genetic differentiation (Q(ST)) is commonly used to test for signatures of selection in population divergence. However, there is an ongoing discussion about what F-ST actually measures, even resulting in some alternative metrics to express neutral genetic differentiation. If there is a problem with F-ST, this could have repercussions for its comparison with Q(ST) as well. We show that as the mutation rate of the neutral marker increases, F-ST decreases: a higher within-population heterozygosity (He) yields a lower F-ST value. However, the same is true for Q(ST): a higher mutation rate for the underlying QTL also results in a lower Q(ST) estimate. The effect of mutation rate is equivalent in Q(ST) and F-ST. Hence, the comparison between Q(ST) and F-ST remains valid, if one uses neutral markers whose mutation rates are not too high compared to those of quantitative traits. Usage of highly variable neutral markers such as hypervariable microsatellites can lead to serious biases and the incorrect inference that divergent selection has acted on populations. Much of the discussion on F-ST seems to stem from the misunderstanding that it measures the differentiation of populations, whereas it actually measures the fixation of alleles. In their capacity as measures of population differentiation, Hedrick's G'(ST) and Jost's D reach their maximum value of 1 when populations do not share alleles even when there remains variation within populations, which invalidates them for comparisons with Q(ST).

  • 32.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Sæther, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Grahn, Mats
    Fiske, Peder
    Kålås, John Atle
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Major histocompatibility complex variation and mate choice in a lekking bird, the great snipe (Gallinago media)2004In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, no 12, p. 3821-3828Article in journal (Refereed)
    Abstract [en]

    Genes of the major histocompatibility complex (MHC) play a major part in the activation of the vertebrate immune system. In addition, they also appear to function as cues for mate choice. In mammals especially, several kinds of MHC-dependent mate choice have been hypothesized and observed. These include choice of mates that share no or few alleles with the choosing individual, choice of mates with alleles that differ as much as possible from the choosing individual, choice of heterozygous mates, choice of certain genotypes and choice of rare alleles. We investigated these different aspects of mate choice in relation to MHC in a lekking bird species, the great snipe (Gallinago media). We found no evidence for MHC disassortative mating, no preference for males with many MHC alleles and no preference for rare alleles. However, we did find that some allelic lineages were more often found in males with mating success than in males without mating success. Females do not seem to use themselves as references for the MHC-dependent mate choice, rather they seem to prefer males with certain allele types. We speculate that these alleles may be linked to resistance to common parasites.

  • 33.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Sæther, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Jacobsson, Pär
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Fiske, Peder
    Sahlman, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Grahn, Mats
    Kålås, John Atle
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Spatial pattern of MHC class II variation in the great snipe (Gallinago media)2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 7, p. 1439-1451Article in journal (Refereed)
    Abstract [en]

    The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism.

  • 34.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Comparative genomics and the study of evolution by natural selection2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 21, p. 4586-4596Article, review/survey (Refereed)
    Abstract [en]

    Genomics profoundly affects most areas of biology, including ecology and evolutionary biology. By examining genome sequences from multiple species, comparative genomics offers new insight into genome evolution and the way natural selection moulds DNA sequence evolution. Functional divergence, as manifested in the accumulation of nonsynonymous substitutions in protein-coding genes, differs among lineages in a manner seemingly related to population size. For example, the ratio of nonsynonymous to synonymous substitution (d(N)/d(S)) is higher in apes than in rodents, compatible with Ohta's nearly neutral theory of molecular evolution, which suggests that the fixation of slightly deleterious mutations contributes to protein evolution at an extent negatively correlated with effective population size. While this supports the idea that functional evolution is not necessarily adaptive, comparative genomics is uncovering a role for positive Darwinian selection in 10-40% of all genes in different lineages, estimates that are likely to increase when the addition of more genomes gives increased power. Again, population size seems to matter also in this context, with a higher proportion of fixed amino acid changes representing advantageous mutations in large populations. Genes that are particularly prone to be driven by positive selection include those involved with reproduction, immune response, sensory perception and apoptosis. Genetic innovations are also frequently obtained by the gain or loss of complete gene sequences. Moreover, it is increasingly realized, from comparative genomics, that purifying selection conserves much more than just the protein-coding part of the genome, and this points at an important role for regulatory elements in trait evolution. Finally, genome sequencing using outbred or multiple individuals has provided a wealth of polymorphism data that gives information on population history, demography and marker evolution.

  • 35.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Sequencing goes 454 and takes large-scale genomics into the wild2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 7, p. 1629-1631Article in journal (Refereed)
    Abstract [en]

    Sometimes, science takes a big leap forward. This is often due to new technology that allows the study of questions previously difficult or even impossible to address. An example of this is provided in this issue (Vera et al. 2008) by the first large-scale attempt toward genome sequencing of an ecologically important model, based on the new '454-sequencing technology'. Using this new technology, the protein-coding sequences of the Glanville fritillary butterfly genome have now been largely characterized.

  • 36.
    Ellis, Thomas James
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Gregor Mendel Inst Mol Plant Sci, Vienna, Austria.
    Postma, Froukje M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Oakley, Christopher G.
    Purdue Univ, Dept Bot & Plant Pathol, W Lafayette, IN 47907 USA.;Purdue Univ, Ctr Plant Biol, W Lafayette, IN 47907 USA.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Life-history trade-offs and the genetic basis of fitness in Arabidopsis thaliana2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 12, p. 2846-2858Article in journal (Refereed)
    Abstract [en]

    Resources allocated to survival cannot be used to increase fecundity, but the extent to which this trade-off constrains adaptation depends on overall resource status. Adaptation to local environmental conditions may therefore entail the evolution of traits that increase the amount of resources available to individuals (their resource status or ‘condition’). We examined the relative contribution of trade-offs and increased condition to adaptive evolution in a recombinant inbred line population of Arabidopsis thaliana planted at the native sites of the parental ecotypes in Italy and Sweden in 2 years. We estimated genetic correlations among fitness components based on genotypic means and explored their causes with QTL mapping. The local ecotype produced more seeds per fruit than did the non-local ecotype, reflected in stronger adaptive differentiation than was previously shown based on survival and fruit number only. Genetic correlations between survival and overall fecundity, and between number of fruits and number of seeds per fruit, were positive, and there was little evidence of a trade-off between seed size and number. Quantitative trait loci for these traits tended to map to the same regions of the genome and showed positive pleiotropic effects. The results indicate that adaptive differentiation between the two focal populations largely reflects the evolution of increased ability to acquire resources in the local environment, rather than shifts in the relative allocation to different life-history traits. Differentiation both in phenology and in tolerance to cold is likely to contribute to the advantage of the local genotype at the two sites.

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  • 37.
    Ferreira, Mafalda S.
    et al.
    CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal;Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal.
    Alves, Paulo C.
    CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal;Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal;Wildlife Biology Program University of Montana Missoula MT USA.
    Callahan, Colin M.
    Division of Biological Sciences University of Montana Missoula MT USA.
    Marques, João P.
    CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal;Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal.
    Mills, L. Scott
    Wildlife Biology Program University of Montana Missoula MT USA;Department of Forestry and Environmental Resources Fisheries, Wildlife and Conservation Biology Program North Carolina State University Raleigh NC USA.
    Good, Jeffrey M.
    Division of Biological Sciences University of Montana Missoula MT USA.
    Melo-Ferreira, José
    CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal;Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal.
    The transcriptional landscape of seasonal coat colour moult in the snowshoe hare2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 16, p. 4173-4185Article in journal (Refereed)
    Abstract [en]

    Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study, we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA sequencing, we tested whether patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. “White” pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional “intermediate” and “brown” pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of nonmodel organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits.

  • 38. Fijarczyk, Anna
    et al.
    Nadachowska, Krystyna
    Jagiellonian University.
    Hofman, Sebastian
    Litvinchuk, Spartak N.
    Babik, Wieslaw
    Stuglik, Michal
    Gollmann, Günter
    Choleva, Lukás
    Cogălniceanu, Dan
    Vukov, Tanja
    Džukic, George
    Szymura, Jacek M.
    Nuclear and mitochondrial phylogeography of the European fire‐bellied toads Bombina bombina and Bombina variegata supports their independent histories2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 16, p. 3381-3398Article in journal (Refereed)
    Abstract [en]

    Exact location and number of glacial refugia still remain unclear for many European cold-blooded terrestrial vertebrates. We performed a fine-scaled multilocus phylogeographic analysis of two Bombina species combining mitochondrial variation of 950 toads from 385 sites and nuclear genes (Rag-1, Ncx-1) from a subset of samples to reconstruct their colonization and contemporary variation patterns. We identified the lowlands northwest of the Black Sea and the Carpathians to be important refugial areas for B. bombina and B. variegata,respectively. This result emphasizes the importance of Central European refugia for ectothermic terrestrial species, far north of the Mediterranean areas regarded as exclusive glacial refugia for the animals. Additional refugia for B. variegata have been located in the southern Apennines and Balkans. In contrast, no evidence for the importance of other east European plains as refugial regions has been found. The distribution of mtDNA and Ncx-1 variation suggests the presence of local refugia near the Black Sea for B. bombina; however, coalescent simulations did not allow to distinguish whether one or two refugia were present in the region. Strong genetic drift apparently accompanied postglacial expansions reducing diversity in the colonization areas. Extended sampling, coupled with the multilocus isolation with migration analysis, revealed a limited and geographically restricted gene flow from the Balkan to Carpathian populations ofB. variegata. However, despite proximity of inferred B. bombina and B. variegata refugia, gene exchange between them was not detected.

  • 39. Florin, Ann-Britt
    et al.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Absence of population structure of turbot (Psetta maxima) in the Baltic Sea2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 1, p. 115-126Article in journal (Refereed)
    Abstract [en]

    We found low, albeit significant, genetic differentiation among turbot (Psetta maxima) in the Baltic Sea but in contrast to earlier findings we found no evidence of isolation by distance. In fact temporal variation among years in one locality exceeded spatial variation among localities. This is an unexpected result since adult turbot are sedentary and eggs are demersal at the salinities occurring in the Baltic. Our findings are most likely explained by the fact that we sampled fish that were born after/during a large influx of water to the Baltic Sea, which may have had the consequence that previously locally and relatively sedentary populations became admixed. These results suggest that populations that colonize relatively variable habitats, like the Baltic, face problems. Any adaptations to local conditions that may build up during stable periods may quickly become eroded when conditions change and/or when populations become admixed. Our results indicate that the ability of turbot to survive and reproduce at the low salinity in the Baltic is more likely due to phenotypic plasticity than a strict genetic adaptation to low salinity.

  • 40.
    Foote, Andrew D.
    et al.
    Univ Bern, Inst Ecol & Evolut, CMPG, Baltzerstr 6, CH-3012 Bern, Switzerland.
    Martin, Michael D.
    NTNU Univ Museum, Trondheim, Norway.
    Louis, Marie
    Univ Copenhagen, Dept Biol, Sect Evolutionary Genom, Copenhagen, Denmark;Univ St Andrews, East Sands, Scottish Oceans Inst, St Andrews, Fife, Scotland.
    Pacheco, George
    Univ Copenhagen, Dept Biol, Sect Evolutionary Genom, Copenhagen, Denmark.
    Robertson, Kelly M.
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Sinding, Mikkel-Holger S.
    Univ Copenhagen, Dept Biol, Sect Evolutionary Genom, Copenhagen, Denmark;Greenland Inst Nat Resources, Nuuk, Greenland.
    Amaral, Ana R.
    Amer Museum Nat Hist, New York, NY 10024 USA;Univ Lisbon, Fac Ciencias, Ctr Ecol Evolut & Environm Changes, Lisbon, Portugal.
    Baird, Robin W.
    Cascadia Res, Olympia, WA USA.
    Baker, Charles Scott
    Oregon State Univ, Marine Mammal Inst, Dept Fisheries & Wildlife, Newport, OR USA;Univ Auckland, Sch Biol Sci, Auckland, New Zealand.
    Ballance, Lisa
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Barlow, Jay
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Brownlow, Andrew
    SRUC Vet Serv Drummondhill, Scottish Marine Anim Stranding Scheme, Inverness, Scotland.
    Collins, Tim
    Wildlife Conservat Soc, Ocean Giants Program, New York, NY USA.
    Constantine, Rochelle
    Univ Auckland, Sch Biol Sci, Auckland, New Zealand.
    Dabin, Willy
    Univ La Rochelle, CNRS, Observ Pelagis, La Rochelle, France.
    Dalla Rosa, Luciano
    Univ Fed Rio Grande, Inst Oceanog, Lab Ecol & Conservacao Megafauna Marinha, Rio Grande, Brazil.
    Davison, Nicholas J.
    SRUC Vet Serv Drummondhill, Scottish Marine Anim Stranding Scheme, Inverness, Scotland.
    Durban, John W.
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Esteban, Ruth
    CIRCE Conservat Informat & Res Cetaceans, Algeciras, Spain.
    Ferguson, Steven H.
    Fisheries & Oceans Canada, Winnipeg, MB, Canada.
    Gerrodette, Tim
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Guinet, Christophe
    CNRS ULR, CEBC, UMR, Chize, France.
    Hanson, M. Bradley
    NOAA, Natl Marine Fisheries Serv, Northwest Fisheries Sci Ctr, Seattle, WA 98115 USA.
    Hoggard, Wayne
    NOAA, Natl Marine Fisheries Serv, Southeast Fisheries Sci Ctr, Pascagoula, MS USA.
    Matthews, Cory J. D.
    Fisheries & Oceans Canada, Winnipeg, MB, Canada.
    Samarra, Filipa I. P.
    Marine & Freshwater Res Inst, Reykjavik, Iceland.
    de Stephanis, Renaud
    CIRCE Conservat Informat & Res Cetaceans, Algeciras, Spain.
    Tavares, Sara B.
    Univ St Andrews, East Sands, Scottish Oceans Inst, St Andrews, Fife, Scotland.
    Tixier, Paul
    CNRS ULR, CEBC, UMR, Chize, France;Deakin Univ, Sch Life & Environm Sci, Burwood Campus, Geelong, Vic, Australia.
    Totterdell, John A.
    Marine Informat & Res Grp Australia MIRG, Quinns Rocks, WA, Australia.
    Wade, Paul
    NOAA, Natl Marine Mammal Lab, Natl Marine Fisheries Serv, Alaska Fisheries Sci Ctr, Washington, DC USA.
    Excoffier, Laurent
    Univ Bern, Inst Ecol & Evolut, CMPG, Baltzerstr 6, CH-3012 Bern, Switzerland.
    Gilbert, M. Thomas P.
    NTNU Univ Museum, Trondheim, Norway;Univ Copenhagen, Dept Biol, Sect Evolutionary Genom, Copenhagen, Denmark.
    Wolf, Jochen B. W.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany.
    Morin, Phillip A.
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Killer whale genomes reveal a complex history of recurrent admixture and vicariance2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 14, p. 3427-3444Article in journal (Refereed)
    Abstract [en]

    Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to fourfold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

  • 41. Forstmeier, Wolfgang
    et al.
    Schielzeth, Holger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mueller, Jakob C.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kempenaers, Bart
    Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 13, p. 3237-3249Article in journal (Refereed)
    Abstract [en]

    Numerous studies have reported associations between heterozygosity in microsatellite markers and fitness-related traits (heterozygosityfitness correlations, HFCs). However, it has often been questioned whether HFCs reflect general inbreeding depression, because a small panel of microsatellite markers does not reflect very well an individuals inbreeding coefficient (F) as calculated from a pedigree. Here, we challenge this prevailing view. Because of chance events during Mendelian segregation, an individuals realized proportion of the genome that is identical by descent (IBD) may substantially deviate from the pedigree-based expectation (i.e. F). This Mendelian noise may result in a weak correlation between F and multi-locus heterozygosity, but this does not imply that multi-locus heterozygosity is a bad estimator of realized IBD. We examined correlations between 11 fitness-related traits measured in up to 1192 captive zebra finches and three measures of inbreeding: (i) heterozygosity across 11 microsatellite markers, (ii) heterozygosity across 1359 single-nucleotide polymorphism (SNP) markers and (iii) F, based on a 5th-generation pedigree. All 11 phenotypic traits showed positive relationships with measures of heterozygosity, especially traits that are most closely related to fitness. Remarkably, the small panel of microsatellite markers produced equally strong HFCs as the large panel of SNP markers. Both marker-based approaches produced stronger correlations with phenotypes than the pedigree-based F, and this did not seem to result from the shortness of our pedigree. We argue that a small panel of microsatellites with high allelic richness may better reflect an individuals realized IBD than previously appreciated, especially in species like the zebra finch, where much of the genome is inherited in large blocks that rarely experience cross-over during meiosis.

  • 42.
    Fountain‐Jones, Nicholas M.
    et al.
    School of Natural Sciences University of Tasmania Hobart Tasmania Australia.
    Giraud, Tatiana
    Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680 Université Paris‐Saclay, CNRS, AgroParisTech Gif‐sur‐Yvette France.
    Zinger, Lucie
    Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure CNRS, INSERM, PSL Université Paris Paris France;Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, CNRS, Institut de Recherche pour le Développement (IRD) Université Toulouse 3 Paul Sabatier Toulouse France.
    Bik, Holly
    Department of Marine Sciences and Institute of Bioinformatics University of Georgia Athens Georgia USA.
    Creer, Simon
    School of Environmental and Natural Sciences Bangor University Bangor UK.
    Videvall, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Department of Ecology, Evolution and Organismal Biology Brown University Providence Rhode Island USA;Institute at Brown for Environment and Society Brown University Providence Rhode Island USA.
    Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions2024In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 33, no 2Article in journal (Refereed)
    Abstract [en]

    The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.

  • 43. Galtier, N.
    et al.
    Nabholz, Benoit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Glemin, S.
    Hurst, G. D. D.
    Mitochondrial DNA as a marker of molecular diversity: a reappraisal2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, no 22, p. 4541-4550Article, review/survey (Refereed)
    Abstract [en]

    Over the last three decades, mitochondrial DNA has been the most popular marker of molecular diversity, for a combination of technical ease-of-use considerations, and supposed biological and evolutionary properties of clonality, near-neutrality and clock-like nature of its substitution rate. Reviewing recent literature on the subject, we argue that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like, questioning its relevance as a witness of recent species and population history. We critically evaluate the usage of mitochondrial DNA for species delineation and identification. Finally, we note the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome.

  • 44.
    Garcia, Sarahi L.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    McMahon, Katherine D.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.;Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA..
    Grossart, Hans-Peter
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, D-16775 Ot Neuglobsow, Stechlin, Germany.;Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany..
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Warnecke, Falk
    Univ Jena, Jena Sch Microbial Commun, D-07743 Jena, Germany..
    Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 17, p. 4449-4459Article in journal (Refereed)
    Abstract [en]

    Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.

  • 45.
    Garcia-Berro, Aurora
    et al.
    CSIC Ajuntament Barcelona, Inst Bot Barcelona IBB, Barcelona, Catalonia, Spain..
    Talla, Venkat
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vila, Roger
    Univ Pompeu Fabra, Inst Biol Evolut, CSIC, Barcelona, Spain..
    Wai, Hong Kar
    Monash Univ Malaysia, Jeffrey Cheah Sch Med & Hlth Sci, Novel Bacteria & Drug Discovery Res Grp NBDD, Selangor Darul Ehsan, Malaysia.;Monash Univ Malaysia, Jeffrey Cheah Sch Med & Hlth Sci, Microbiome & Bioresource Res Strength MBRS, Selangor Darul Ehsan, Malaysia.;Univ Malaya, Inst Biol Sci, Div Genet & Mol Biol, Kuala Lumpur, Malaysia..
    Shipilina, Daria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Swedish Collegium for Advanced Study (SCAS).
    Chan, Kok Gan
    Univ Malaya, Inst Biol Sci, Div Genet & Mol Biol, Kuala Lumpur, Malaysia.;Jiangsu Univ, Int Genome Ctr, Zhenjiang, Jiangsu, Peoples R China.;Shantou Univ, Inst Marine Sci, Guangdong Prov Key Lab Marine Biol, Shantou, Peoples R China..
    Pierce, Naomi E.
    Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA.;Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA..
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Talavera, Gerard
    CSIC Ajuntament Barcelona, Inst Bot Barcelona IBB, Barcelona, Catalonia, Spain.;Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA.;Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA..
    Migratory behaviour is positively associated with genetic diversity in butterflies2023In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 3, p. 560-574Article in journal (Refereed)
    Abstract [en]

    Migration is typically associated with risk and uncertainty at the population level, but little is known about its cost–benefit trade-offs at the species level. Migratory insects in particular often exhibit strong demographic fluctuations due to local bottlenecks and outbreaks. Here, we use genomic data to investigate levels of heterozygosity and long-term population size dynamics in migratory insects, as an alternative to classical local and short-term approaches such as regional field monitoring. We analyse whole-genome sequences from 97 Lepidoptera species and show that individuals of migratory species have significantly higher levels of genome-wide heterozygosity, a proxy for effective population size, than do nonmigratory species. Also, we contribute whole-genome data for one of the most emblematic insect migratory species, the painted lady butterfly (Vanessa cardui), sampled across its worldwide distributional range. This species exhibits one of the highest levels of genomic heterozygosity described in Lepidoptera (2.95 ± 0.15%). Coalescent modelling (PSMC) shows historical demographic stability in V. cardui, and high effective population size estimates of 2–20 million individuals 10,000 years ago. The study reveals that the high risks associated with migration and local environmental fluctuations do not seem to decrease overall genetic diversity and demographic stability in migratory Lepidoptera. We propose a “compensatory” demographic model for migratory r-strategist organisms in which local bottlenecks are counterbalanced by reproductive success elsewhere within their typically large distributional ranges. Our findings highlight that the boundaries of populations are substantially different for sedentary and migratory insects, and that, in the latter, local and even regional field monitoring results may not reflect whole population dynamics. Genomic diversity patterns may elucidate key aspects of an insect's migratory nature and population dynamics at large spatiotemporal scales.

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  • 46. Geffen, Eli
    et al.
    Waidyaratne, Sitara
    Dalén, Love
    Angerbjörn, Anders
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hersteinsson, Pall
    Fuglei, Eva
    White, Paula A.
    Goltsman, Michael
    Kapel, Christian M.
    Wayne, Robert K.
    Sea ice occurrence predicts genetic isolation in the Arctic fox2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 20, p. 4241-4255Article in journal (Refereed)
    Abstract [en]

    Unlike Oceanic islands, the islands of the Arctic Sea are not completely isolated from migration by terrestrial vertebrates. The pack ice connects many Arctic Sea islands to the mainland during winter months. The Arctic fox (Alopex lagopus), which has a circumpolar distribution, populates numerous islands in the Arctic Sea. In this study, we used genetic data from 20 different populations, spanning the entire distribution of the Arctic fox, to identify barriers to dispersal. Specifically, we considered geographical distance, occurrence of sea ice, winter temperature, ecotype, and the presence of red fox and polar bear as nonexclusive factors that influence the dispersal behaviour of individuals. Using distance-based redundancy analysis and the BIOENV procedure, we showed that occurrence of sea ice is the key predictor and explained 40-60% of the genetic distance among populations. In addition, our analysis identified the Commander and Pribilof Islands Arctic populations as genetically unique suggesting they deserve special attention from a conservation perspective.

  • 47. Griekspoor, Petra
    et al.
    Colles, Frances M
    McCarthy, Noel D
    Hansbro, Philip M
    Ashhurst-Smith, Chris
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Hasselquist, Dennis
    Maiden, Martin C J
    Waldenström, Jonas
    Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 5, p. 1463-1472Article in journal (Refereed)
    Abstract [en]

    Zoonotic pathogens often infect several animal species, and gene flow among populations infecting different host species may affect the biological traits of the pathogen including host specificity, transmissibility and virulence. The bacterium Campylobacter jejuni is a widespread zoonotic multihost pathogen, which frequently causes gastroenteritis in humans. Poultry products are important transmission vehicles to humans, but the bacterium is common in other domestic and wild animals, particularly birds, which are a potential infection source. Population genetic studies of C. jejuni have mainly investigated isolates from humans and domestic animals, so to assess C. jejuni population structure more broadly and investigate host adaptation, 928 wild bird isolates from Europe and Australia were genotyped by multilocus sequencing and compared to the genotypes recovered from 1366 domestic animal and human isolates. Campylobacter jejuni populations from different wild bird species were distinct from each other and from those from domestic animals and humans, and the host species of wild bird was the major determinant of C. jejuni genotype, while geographic origin was of little importance. By comparison, C. jejuni differentiation was restricted between more phylogenetically diverse farm animals, indicating that domesticated animals may represent a novel niche for C. jejuni and thereby driving the evolution of those bacteria as they exploit this niche. Human disease is dominated by isolates from this novel domesticated animal niche.

  • 48.
    Griesser, Michael
    et al.
    Univ Zurich, Anthropol Inst & Museum, CH-8057 Zurich, Switzerland..
    Halvarsson, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Drobniak, Szymon M.
    Univ Zurich, Anthropol Inst & Museum, CH-8057 Zurich, Switzerland..
    Vila, Carles
    CSIC, EBD, Conservat & Evolutionary Genet Grp, E-41080 Seville, Spain..
    Fine-scale kin recognition in the absence of social familiarity in the Siberian jay, a monogamous bird species2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 22, p. 5726-5738Article in journal (Refereed)
    Abstract [en]

    Kin recognition is a critical element to kin cooperation, and in vertebrates, it is primarily based on associative learning. Recognition of socially unfamiliar kin occurs rarely, and it is reported only in vertebrate species where promiscuity prevents recognition of first-order relatives. However, it is unknown whether the recognition of socially unfamiliar kin can evolve in monogamous species. Here, we investigate whether genetic relatedness modulates aggression among group members in Siberian jays (Perisoreus infaustus). This bird species is genetically and socially monogamous and lives in groups that are formed through the retention of offspring beyond independence, and the immigration of socially unfamiliar nonbreeders. Observations on feeders showed that genetic relatedness modulated aggression of breeders towards immigrants in a graded manner, in that they chased most intensely the immigrant group members that were genetically the least related. However, cross-fostering experiments showed that breeders were equally tolerant towards their own and cross-fostered young swapped as nestlings. Thus, breeders seem to use different mechanisms to recognize socially unfamiliar individuals and own offspring. As Siberian jays show a high degree of nepotism during foraging and predator encounters, inclusive fitness benefits may play a role for the evolution of fine-scale kin recognition. More generally, our results suggest that fine-graded kin recognition can evolve independently of social familiarity, highlighting the evolutionary importance of kin recognition for social species.

  • 49.
    Grosser, Stefanie
    et al.
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany;Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany.
    Sauer, Jan
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany.
    Paijmans, Anneke J.
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany.
    Caspers, Barbara A.
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany.
    Forcada, Jaume
    NERC, British Antarctic Survey, Cambridge, England.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany.
    Hoffman, Joseph I.
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany;NERC, British Antarctic Survey, Cambridge, England.
    Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 9, p. 2406-2422Article in journal (Refereed)
    Abstract [en]

    Despite an increasing appreciation of the importance of host-microbe interactions in ecological and evolutionary processes, the factors shaping microbial communities in wild populations remain poorly understood. We therefore exploited a natural experiment provided by two adjacent Antarctic fur seal (Arctocephalus gazella) colonies of high and low social density and combined 16S rRNA metabarcoding with microsatellite profiling of mother-offspring pairs to investigate environmental and genetic influences on skin microbial communities. Seal-associated bacterial communities differed profoundly between the two colonies, despite the host populations themselves being genetically undifferentiated. Consistent with the hypothesis that social stress depresses bacterial diversity, we found that microbial alpha diversity was significantly lower in the high-density colony. Seals from one of the colonies that contained a stream also carried a subset of freshwater-associated bacteria, indicative of an influence of the physical environment. Furthermore, mothers and their offspring shared similar microbial communities, in support of the notion that microbes may facilitate mother-offspring recognition. Finally, a significant negative association was found between bacterial diversity and heterozygosity, a measure of host genetic quality. Our study thus reveals a complex interplay between environmental and host genetic effects, while also providing empirical support for the leash model of host control, which posits that bacterial communities are driven not only by bottom-up species interactions, but also by top-down host regulation. Taken together, our findings have broad implications for understanding host-microbe interactions as well as prokaryotic diversity in general.

  • 50.
    Gunnarsson, Urban
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Ecological Botany.
    Shaw, A.J.
    Lönn, Mikael
    Local-scale genetic structure in the peatmoss Sphagnum fuscum2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 2, p. 305-312Article in journal (Refereed)
    Abstract [en]

    Sphagnum (peatmoss) dominates huge areas of the Northern Hemisphere and acts as a significant carbon sink on a global scale, yet little is known about the genetic structure of Sphagnum populations. We investigated genetic structure within a population of the common peatmoss Sphagnum fuscum, to assess local patterns of genetic diversity and the spatial extent of clones. One hundred seventeen shoots were sampled from five transects in Fuglmyra, central Norway, and sequenced for three anonymous DNA regions. Five neighbourhood patches were marked along each transect, and from each patch, five stems were sampled for molecular analyses. Seventeen haplotypes could be distinguished and two major groups of haplotypes differed by 12 mutational steps. The two major haplotype groups differed significantly in microhabitat association along the distance to groundwater table and the pH gradients, indicating microhabitat differentiation. The haplotypes within these groups were all genetically similar, differing by one or two mutations. The most common haplotype occurred in four transects separated by 250-m distance. Most of the molecular variation in the population was found among transects, and within patches. Large dominating clones within each transect resulted in low variation explained by the among-patch-within-transect component of spatial structure. Mutation appears to account for a larger proportion of the population variation than recombination. Within the population, vegetative growth and asexual reproduction from gametophyte fragments dominate as the main reproductive mode.

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