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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.

  • 2. Allendorf, Fred W.
    et al.
    Berry, Oliver
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    So long to genetic diversity, and thanks for all the fish2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 1, p. 23-25Article in journal (Refereed)
    Abstract [en]

    The world faces a global fishing crisis. Wild marine fisheries comprise nearly 15% of all animal protein in the human diet, but, according to the U.N. Food and Agriculture Organization, nearly 60% of all commercially important marine fish stocks are overexploited, recovering, or depleted (FAO 2012; Fig. 1). Some authors have suggested that the large population sizes of harvested marine fish make even collapsed populations resistant to the loss of genetic variation by genetic drift (e. g. Beverton 1990). In contrast, others have argued that the loss of alleles because of overfishing may actually be more dramatic in large populations than in small ones (Ryman et al. 1995). In this issue, Pinsky & Palumbi (2014) report that overfished populations have approximately 2% lower heterozygosity and 12% lower allelic richness than populations that are not overfished. They also performed simulations which suggest that their estimates likely underestimate the actual loss of rare alleles by a factor of three or four. This important paper shows that the harvesting of marine fish can have genetic effects that threaten the long-term sustainability of this valuable resource.

  • 3. Alsos, I G
    et al.
    Engelskjon, T
    Gielly, L
    Taberlet, P
    Brochmann, C
    Impact of ice ages on circumpolar molecular diversity: insights from an ecological key species2005In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 14, no 9, p. 2739-2753Article in journal (Refereed)
    Abstract [en]

    We address the impact of the ice age cycles on intraspecific cpDNA diversity, for the first time on the full circumboreal-circumarctic scale. The bird-dispersed bog bilberry (or arctic blueberry, Vaccinium uliginosum) is a key component of northern ecosystems and is here used to assess diversity in previously glaciated vs. unglaciated areas and the importance of Beringia as a refugium and source for interglacial expansion. Eighteen chloroplast DNA haplotypes were observed in and among 122 populations, grouping into three main lineages which probably diverged before, and thus were affected more or less independently by, all major glaciations. The boreal ‘Amphi-Atlantic lineage’ included one haplotype occurring throughout northern Europe and one occurring in eastern North America, suggesting expansion from at least two bottlenecked, glacial refugium populations. The boreal ‘Beringian lineage’ included seven haplotypes restricted to Beringia and the Pacific coast of USA. The ‘Arctic-Alpine lineage’ included nine haplotypes, one of them fully circumpolar. This lineage was unexpectedly diverse, also in previously glaciated areas, suggesting that it thrived on the vast tundras during the ice ages and recolonized deglaciated terrain over long distances. Its largest area of persistence during glaciations was probably situated in the north, stretching from Beringia and far into Eurasia, and it probably also survived the last glaciation in southern mountain ranges. Although Beringia apparently was important for the initial divergence and expansion of V. uliginosum as well as for continuous survival of both the Beringian and Arctic-Alpine lineages during all ice ages, this region played a minor role as a source for later interglacial expansions.

  • 4.
    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.

  • 5.
    Anderholm, Sofia
    et al.
    University of Gothenburg.
    Waldeck, Peter
    University of Gothenburg.
    van der Jeugd, Henk P
    Netherlands Institute for Ecology (NIOO-KNAW), The Netherlands.
    Marshall, Rupert C
    University of Gothenburg ; Aberystwyth University, UK.
    Larsson, Kjell
    Gotland University.
    Andersson, Malte
    University of Gothenburg.
    Colony kin structure and host-parasite relatedness in the barnacle goose2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, no 23, p. 4955-4963Article in journal (Refereed)
    Abstract [en]

    Conspecific brood parasitism (CBP), females laying eggs in the nest of other 'host' females of the same species, is a common alternative reproductive tactic among birds. For hosts there are likely costs of incubating and rearing foreign offspring, but costs may be low in species with precocial chicks such as waterfowl, among which CBP is common. Waterfowl show strong female natal philopatry, and spatial relatedness among females may influence the evolution of CBP. Here we investigate fine-scale kin structure in a Baltic colony of barnacle geese, Branta leucopsis, estimating female spatial relatedness using protein fingerprints of egg albumen, and testing the performance of this estimator in known mother-daughter pairs. Relatedness was significantly higher between neighbour females (nesting ≤ 40 metres from each other) than between females nesting farther apart, but there was no further distance trend in relatedness. This pattern may be explained by earlier observations of females nesting close to their mother or brood sisters, even when far from the birth nest. Hosts and parasites were on average not more closely related than neighbour females. In 25 of 35 sampled parasitized nests, parasitic eggs were laid after the host female finished laying, too late to develop and hatch. Timely parasites, laying eggs in the host's laying sequence, had similar relatedness to hosts as that between neighbours. Females laying late parasitic eggs tended to be less related to the host, but not significantly so. Our results suggest that CBP in barnacle geese might represent different tactical life-history responses.

  • 6. 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.

  • 7.
    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.

  • 8.
    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.

  • 9.
    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.

  • 10. 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.

  • 11. Bensch, Staffan
    et al.
    Grahn, Mats
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Environmental science.
    Müller, Nils
    Gay, Laurene
    Åkesson, Susanne
    Genetic, morphological, and feather isotope variation of migratory willow warblers show gradual divergence in a ring.2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, no 14, p. 3087-96Article in journal (Refereed)
    Abstract [en]

    The circular distribution of the willow warbler Phylloscopus trochilus around the Baltic Sea shares many features with the classic examples of ring species; however, the system is much younger. It has previously been shown that a secondary contact zone is located in central Scandinavia, where there are narrow clines for several morphological traits coincident with a migratory divide. Here we analyse multiple traits and genes from > 1700 males captured on breeding territories at 77 sites spread around the Baltic Sea to test the following hypothesis. If the secondary contact zone in Scandinavia is a result of divergence in two allopatric refuge populations during the last glaciation, we expect to find a similar secondary contact zone somewhere else around the circular distribution. Our results show that the trait clines were wider and displaced from each other along the eastern side of the Baltic Sea. Analyses of 12 microsatellite loci confirmed that the genome is very similar between the terminal forms (F(ST) = 0). Two AFLP-derived markers filtered out from a genomic scan instead appear to be maintained by selection. These markers exhibited steep clines at the secondary contact zone in Scandinavia, but as for the phenotypic traits, had vastly different cline centres east of the Baltic Sea. The trait clines along the ring distribution outside the Scandinavian secondary contact zone thus seem to have been shaped by independent action of selection or drift during the process of postglacial colonization.

  • 12.
    Berasategui, Aileen
    et al.
    Dep. of Biochemistry, Max Planck institute for Chemical Ecology.
    Axelsson, Karolin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Nordlander, Göran
    Dep. of Ecology, SLU.
    Schmidt, Axel
    Max Planck Institute for Chemical Ecology.
    Borg-Karlson, Anna-Karin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Gershenzon, Jonathan
    Dep of Biochemistry, Max Planck institute for Chemical Ecology.
    Terenius, Olle
    Dep of Ecology, SLU.
    Kaltenpoth, Martin
    Insect Symbiosis Research Group, Max Planck institute for Chemical Ecology.
    The Gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 16, p. 4014-4031Article in journal (Refereed)
    Abstract [en]

    The pine weevil (Hylobius abietis, Coleoptera: Curculionidae) is an important pest of conifer seedlings in Europe. Despite its economic importance, little is known about the composition of its gut microbial community and the role it plays in mediating the weevil's ability to utilize conifers as a food source. Here, we characterized the gut bacterial communities of different populations of H. abietis across Europe and compared them to those of other beetles that occupy similar ecological niches. We demonstrate that the microbial community of H. abietis is similar at higher taxonomic levels (family and genus) across locations in Europe, with Wolbachia as the dominant microbe, followed by Enterobacteria and Firmicutes. Despite this similarity, we observed consistent differences between countries and locations, but not sexes. Our meta-analysis demonstrates that the gut bacterial community of the pine weevil is very similar to that of bark beetles that also exploit conifers as a food source. The Enterobacteriaceae symbionts of both host taxa are especially closely related phylogenetically. Conversely, the microbiota of H. abietis is distinct from that of closely related weevils feeding on non-conifer food sources, suggesting that the microbial community of the pine weevil is determined by the environment and may be relevant to host ecology. Furthermore, several H. abietis-associated members of the Enterobacteriaceae family are known to contain genes involved in terpenoid degradation. As such, we hypothesize that the gut microbial community is important for the utilization of conifer seedlings as a food source, either through the detoxification of plant secondary metabolites or supplementation of essential nutrients.

  • 13.
    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.

  • 14.
    Bernhardsson, Carolina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Geographic structure and adaptive population differentiation in herbivore defence genes in European aspen (Populus tremula L., Salicaceae)2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 9, p. 2197-2207Article in journal (Refereed)
    Abstract [en]

    When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling the trait are also expected to show strong patterns of genetic differentiation since alternative alleles are favored in different geographical locations. Here we study 71 SNPs from seven genes associated with inducible defense responses in a sample of P. tremula collected from across Sweden. Four of these genes (PPO2, TI2, TI4 and TI5) show substantial population differentiation and a PCA conducted on the defense SNPs divides the Swedish population into three distinct clusters. Several defense SNPs show latitudinal clines, although these were not robust to multiple testing. However, five SNPs (located within TI4 and TI5) show strong longitudinal clines that remain significant after multiple test correction. Genetic geographical variation, supporting local adaptation, has earlier been confirmed in genes involved in the photoperiod pathway in P. tremula, but this is, to our knowledge, one of the first times that geographic variation has been found in genes involved in plant defense against antagonists.

  • 15.
    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)
  • 16. 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).

  • 17.
    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.

  • 18. Brunhoff, C.
    et al.
    Galbreath, K. E.
    Fedorov, V. B.
    Cook, J. A.
    Jaarola, M.
    Holarctic phylogeography of the root vole (Microtus oeconomus): Implications for late Quaternary biogeography of high latitudes2003In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 12, no 4, p. 957-968Article in journal (Refereed)
    Abstract [en]

    A species-wide phylogeographical study of the root vole (Microtus oeconomus) was performed using the whole 1140 base pair mitochondrial (mt) cytochrome b gene. We examined 83 specimens from 52 localities resulting in 65 unique haplotypes. Our results demonstrate that the root vole is divided into four main mtDNA phylogenetic lineages that seem to have largely allopatric distributions. Net divergence estimates (2.0-3.5%) between phylogroups, as well as relatively high nucleotide diversity estimates within phylogroups, indicate that the distinct phylogeographical structure was initiated by historical events that predated the latest glaciation. European root voles are divided into a Northern and a Central mtDNA phylogroup. The mtDNA data in concert with fossil records imply that root voles remained north of the classical refugial areas in southern Europe during the last glacial period. The currently fragmented populations in central Europe belong to a single mtDNA phylogroup. The Central Asian and the North European lineages are separated by the Ural Mountains, a phylogeographical split also found in collared lemmings (Dicrostonyx) and the common vole (M. arvalis). The Beringian lineage occurs from eastern Russia through Alaska to northwestern Canada. This distribution is congruent with the traditional boundaries of the Beringian refugium and with phylogeographical work on other organisms. In conclusion, similarities between the phylogeographical patterns in the root vole and other rodents, such as Arctic and subarctic lemmings, as well as more temperate vole species, indicate that late Quaternary geological and climatic events played a strong role in structuring northern biotic communities.

  • 19.
    Buechel, Séverine D.
    et al.
    University of Lausanne, Switzerland; Institute of Integrative Biology (IBZ), Switzerland.
    Wurm, Yanick
    Keller, Laurent
    Social chromosome variants differentially affect queen determination and the survival of workers in the fire ant Solenopsis invicta2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 20, p. 5117-5127Article in journal (Refereed)
    Abstract [en]

    Intraspecific variation in social organization is common, yet the underlying causes are rarely known. An exception is the fire ant Solenopsis invicta in which the existence of two distinct forms of social colony organization is under the control of the two variants of a pair of social chromosomes, SB and Sb. Colonies containing exclusively SB/SB workers accept only one single queen and she must be SB/SB. By contrast, when colonies contain more than 10% of SB/Sb workers, they accept several queens but only SB/Sb queens. The variants of the social chromosome are associated with several additional important phenotypic differences, including the size, fecundity and dispersal strategies of queens, aggressiveness of workers, and sperm count in males. However, little is known about whether social chromosome variants affect fitness in other life stages. Here, we perform experiments to determine whether differential selection occurs during development and in adult workers. We find evidence that the Sb variant of the social chromosome increases the likelihood of female brood to develop into queens and that adult SB/Sb workers, the workers that cull SB/SB queens, are overrepresented in comparison to SB/SB workers. This demonstrates that supergenes such as the social chromosome can have complex effects on phenotypes at various stages of development.

  • 20. Cahill, James A
    et al.
    Stirling, Ian
    Kistler, Logan
    Salamzade, Rauf
    Ersmark, Erik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Stockholms Universitet.
    Fulton, Tara L
    Stiller, Mathias
    Green, Richard E
    Shapiro, Beth
    Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed)
    Abstract [en]

    Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof, and Chichagof Islands (ABC Islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC Islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC Islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. This article is protected by copyright. All rights reserved.

  • 21. 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.

  • 22.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Vogel, Heiko
    Söderlind, Lina
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 19, p. 4884-4895Article in journal (Refereed)
    Abstract [en]

    Transcriptome studies of insect herbivory are still rare, yet studies in model systems have uncovered patterns of transcript regulation that appear to provide insights into how insect herbivores attain polyphagy, such as a general increase in expression breadth and regulation of ribosomal, digestion- and detoxification-related genes. We investigated the potential generality of these emerging patterns, in the Swedish comma, Polygonia c-album, which is a polyphagous, widely-distributed butterfly. Urtica dioica and Ribes uva-crispa are hosts of P. c-album, but Ribes represents a recent evolutionary shift onto a very divergent host. Utilizing the assembled transcriptome for read mapping, we assessed gene expression finding that caterpillar life-history (i.e. 2nd vs. 4th-instar regulation) had a limited influence on gene expression plasticity. In contrast, differential expression in response to host-plant identified genes encoding serine-type endopeptidases, membrane-associated proteins and transporters. Differential regulation of genes involved in nucleic acid binding was also observed suggesting that polyphagy involves large scale transcriptional changes. Additionally, transcripts coding for structural constituents of the cuticle were differentially expressed in caterpillars in response to their diet indicating that the insect cuticle may be a target for plant defence. Our results state that emerging patterns of transcript regulation from model species appear relevant in species when placed in an evolutionary context.

  • 23. Chauvet, S
    et al.
    van der Velde, M
    Imbert, E
    Guillemin, ML
    Mayol, M
    Riba, M
    Smulders, MJM
    Vosman, B
    Ericson, L
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Bijlsma, R
    Giles, BE
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Past and current gene flow in the selfing wind-dispersed species Mycelis muralis in western Europe2004In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, no 6, p. 1391-1407Article in journal (Refereed)
    Abstract [en]

    The distribution of genetic diversity in Mycelis muralis, or wall lettuce, was investigated at a European scale using 12 microsatellite markers to infer historical and contemporary forces from genetic patterns. Mycelis muralis has the potential for long-distance seed dispersal by wind, is mainly self-pollinated, and has patchily distributed populations, some of which may show metapopulation dynamics. A total of 359 individuals were sampled from 17 populations located in three regions, designated southern Europe (Spain and France), the Netherlands, and Sweden. At this within-region scale, contemporary evolutionary forces (selfing and metapopulation dynamics) are responsible for high differentiation between populations (0.34 < FST < 0.60) but, contrary to expectation, levels of within-population diversity, estimated by Nei's unbiased expected heterozygosity (HE) (0.24 < HE < 0.68) or analyses of molecular variance (50% of the variation found within-populations), were not low. We suggest that the latter results, which are unusual in selfing species, arise from efficient seed dispersal that counteracts population turnover and thus maintains genetic diversity within populations. At the European scale, northern regions showed lower allelic richness (A = 2.38) than populations from southern Europe (A = 3.34). In light of postglacial colonization hypotheses, these results suggest that rare alleles may have been lost during recolonization northwards. Our results further suggest that mutation has contributed to genetic differentiation between southern and northern Europe, and that Sweden may have been colonized by dispersers originating from at least two different refugia.

  • 24.
    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.

  • 25.
    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.

  • 26. Dalen, L
    et al.
    Elmhagen, B
    Angerbjorn, A
    DNA analysis on fox faeces and competition induced niche shifts2004In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, no 8, p. 2389-2392Article in journal (Refereed)
  • 27. Dalen, L.
    et al.
    Kvaloy, K.
    Linnell, J. D. C.
    Elmhagen, B.
    Strand, O.
    Tannerfeldt, M.
    Henttonen, H.
    Fuglei, E.
    Landa, A.
    Angerbjorn, A.
    Population structure in a critically endangered arctic fox population: does genetics matter?2006In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, no 10, p. 2809-2819Article in journal (Refereed)
  • 28.
    Dalén, Love
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Kvaloy, K.
    Linnell, J. D. C.
    Elmhagen, Bodil
    Stockholm University, Faculty of Science, Department of Zoology.
    Strand, O.
    Tannerfeldt, M.
    Henttonen, H.
    Fuglei, E.
    Landa, A.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Population structure in a critically endangered arctic fox population: does genetics matter?2006In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, no 10, p. 2809-2819Article in journal (Refereed)
    Abstract [en]

    The arctic fox (Alopex lagopus) in Scandinavia is classified as critically endangered after having gone through a severe decline in population size in the beginning of the 20th century, from which it has failed to recover despite more than 65 years of protection. Arctic foxes have a high dispersal rate and often disperse over long distances, suggesting that there was probably little population differentiation within Scandinavia prior to the bottleneck. It is, however, possible that the recent decline in population size has led to a decrease in dispersal and an increase in population fragmentation. To examine this, we used 10 microsatellite loci to analyse genetic variation in 150 arctic foxes from Scandinavia and Russia. The results showed that the arctic fox in Scandinavia presently is subdivided into four populations, and that the Kola Peninsula and northwest Russia together form a large fifth population. Current dispersal between the populations seemed to be very low, but genetic variation within them was relatively high. This and the relative F-ST values among the populations are consistent with a model of recent fragmentation within Scandinavia. Since the amount of genetic variation is high within the populations, but the populations are small and isolated, demographic stochasticity seems to pose a higher threat to the populations' persistence than inbreeding depression and low genetic variation.

  • 29. de Carvalho, Dulcineia
    et al.
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Joseph, Jeffrey
    Suter, Leonie
    Sedivy, Claudio
    Macaya-Sanz, David
    Cottrell, Joan
    Heinze, Berthold
    Schanzer, Ivan
    Lexer, Christian
    Admixture facilitates adaptation from standing variation in the European aspen (P. tremula L.), a widespread forest tree2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 8, p. 1638-1650Article in journal (Refereed)
    Abstract [en]

    Adaptation to new environments can start from new mutations or from standing variation already present in natural populations. Whether admixture constrains or facilitates adaptation from standing variation is largely unknown, especially in ecological keystone or foundation species. We examined patterns of neutral and adaptive population divergence in Populus tremula L., a widespread forest tree, using mapped molecular genetic markers. We detected the genetic signature of postglacial admixture between a Western and an Eastern lineage of P. tremula in Scandinavia, an area suspected to represent a zone of postglacial contact for many species of animals and plants. Stringent divergence-based neutrality tests provided clear indications for locally varying selection at the European scale. Six of 12 polymorphisms under selection were located less than 1 kb away from the nearest gene predicted by the Populus trichocarpa genome sequence. Few of these loci exhibited a signature of 'selective sweeps' in diversity-based tests, which is to be expected if adaptation occurs primarily from standing variation. In Scandinavia, admixture explained genomic patterns of ancestry and the nature of clinal variation and strength of selection for bud set, a phenological trait of great adaptive significance in temperate trees, measured in a common garden trial. Our data provide a hitherto missing direct link between past range shifts because of climatic oscillations, and levels of standing variation currently available for selection and adaptation in a terrestrial foundation species.

  • 30.
    De La Torre, Amanda R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Univ British Columbia, Dept Forest & Conservat Sci, Ctr Forest Conservat Genet, Vancouver, BC V6T 1Z4, Canada.
    Roberts, David R.
    Aitken, Sally N.
    Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 8, p. 2046-2059Article in journal (Refereed)
    Abstract [en]

    The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P.engelmannii in western North America. Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21000years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both F-st outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors.

  • 31.
    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.

  • 32. 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.

  • 33. Desamore, Aurelie
    et al.
    Patino, Jairo
    Mardulyn, Patrick
    Mcdaniel, Stuart F.
    Zanatta, Florian
    Laenen, Benjamin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab). University of Liège, Belgium.
    Vanderpoorten, Alain
    High migration rates shape the postglacial history of amphi-Atlantic bryophytes2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 21, p. 5568-5584Article in journal (Refereed)
    Abstract [en]

    Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework.

  • 34.
    Dibattista, Joseph D.
    et al.
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada .
    Feldheim, Kevin A.
    Field Museum, Pritzker Laboratory for Molecular Systematics and Evolution, Chicago, IL, USA.
    Thibert-Plante, Xavier
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada.
    Gruber, Samuel H.
    Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, Miami, FL, USA.
    Hendry, Andrew P.
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada.
    A genetic assessment of polyandry and breeding-site fidelity in lemon sharks2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 14, p. 3337-3351Article in journal (Refereed)
    Abstract [en]

    We here employ 11 microsatellite markers and recently developed litter reconstruction methods to infer mating system parameters (i.e. polyandry and breeding-site fidelity) at a lemon shark nursery site in Marquesas Key, Florida. Four hundred and eight juvenile or subadult sharks were genotyped over eight complete breeding seasons. Using this information, we were able to infer family structure, as well as fully or partially reconstruct genotypes of 46 mothers and 163 fathers. Multiple litter reconstruction methods were used, and novel simulations helped define apparent bias and precision of at least some mating system parameters. For Marquesas Key, we find that adult female lemon sharks display high levels of polyandry (81% of all litters sampled) and stronger fidelity to the nursery site than do males. Indeed, few male sharks sired offspring from more than one litter during the course of the study. These findings were quite similar to previous results from another lemon shark nursery site (Bimini, Bahamas), suggesting conserved mating system parameters despite significant variation in early life-history traits (i.e. body size and growth) among sites. The finding of at least some site fidelity in females also supports the need for careful conservation of each nursery.

  • 35. 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.

  • 36. Du, Shuhui
    et al.
    Wang, Zhaoshan
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Wang, Dongsheng
    Wang, Junhui
    Wu, Zhiqiang
    Tembrock, Luke R.
    Zhang, Jianguo
    Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 19, p. 4994-5005Article in journal (Refereed)
    Abstract [en]

    Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P.tremula and P.davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P.tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles inthe formation of the disjunct distributions and divergence of these three Populus species.

  • 37. Désamoré, Aurélie
    et al.
    Laenen, Benjamin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Miller, Kelly B.
    Bergsten, Johannes
    Early burst in body size evolution is uncoupled from species diversification in diving beetles (Dytiscidae)2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 4, p. 979-993Article in journal (Refereed)
    Abstract [en]

    Changes in morphology are often thought to be linked to changes in species diversification, which is expected to leave a signal of early burst (EB) in phenotypic traits. However, such signal is rarely recovered in empirical phylogenies, even for groups with well-known adaptive radiation. Using a comprehensive phylogenetic approach in Dytiscidae, which harbours similar to 4,300 species with as much as 50-fold variation in body size among them, we ask whether pattern of species diversification correlates with morphological evolution. Additionally, we test whether the large variation in body size is linked to habitat preference and whether the latter influences species turnover. We found, in sharp contrast to most animal groups, that Dytiscidae body size evolution follows an early-burst model with subsequent high phylogenetic conservatism. However, we found no evidence for associated shifts in species diversification, which point to an uncoupled evolution of morphology and species diversification. We recovered the ancestral habitat of Dytiscidae as lentic (standing water), with many transitions to lotic habitat (running water) that are concomitant to a decrease in body size. Finally, we found no evidence for difference in net diversification rates between habitats nor difference in turnover in lentic and lotic species. This result, together with recent findings in dragonflies, contrasts with some theoretical expectations of the habitat stability hypothesis. Thus, a thorough reassessment of the impact of dispersal, gene flow and range size on the speciation process is needed to fully encompass the evolutionary consequences of the lentic-lotic divide for freshwater fauna.

  • 38.
    Eckstein, Rolf Lutz
    et al.
    Justus-Liebig-University Giessen, Germany.
    O'Neill, R. A.
    Justus-Liebig-University Giessen, Germany.
    Danihelka, J.
    Justus-Liebig-University Giessen, Germany.
    Otte, A.
    Justus-Liebig-University Giessen, Germany.
    Koehler, W.
    Justus-Liebig-University Giessen, Germany.
    Genetic structure among and within peripheral and central populations of three endangered floodplain violets2006In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, no 9, p. 2367-2379Article in journal (Refereed)
    Abstract [en]

    Understanding the partitioning of genetic variance in peripheral and central populations may shed more light on the effects of genetic drift and gene flow on population genetic structure and, thereby, improve attempts to conserve genetic diversity. We analysed genetic structure of peripheral and central populations of three insect-pollinated violets (Viola elatior, Viola pumila, Viola stagnina) to evaluate to what extent these patterns can be explained by gene flow and genetic drift. Amplified fragment length polymorphism was used to analyse 930 individuals of 50 populations. Consistent with theoretical predictions, peripheral populations were smaller and more isolated, differentiation was stronger, and genetic diversity and gene flow lower in peripheral populations of V. pumila and V. stagnina. In V. elatior, probably historic fragmentation effects linked to its specific habitat type were superimposed on the plant geographic (peripheral-central) patterns, resulting in lower relative importance of gene flow in central populations. Genetic variation between regions (3-6%), among (30-37%) and within populations (60-64%) was significant. Peripheral populations lacked markers that were rare and localized in central populations. Loss of widespread markers in peripheral V. stagnina populations indicated genetic erosion. Autocorrelation within populations was statistically significant up to a distance of 10-20 m. Higher average genetic similarity in peripheral populations than in central ones indicated higher local gene flow, probably owing to management practices. Peripheral populations contributed significantly to genetic variation and contained unique markers, which made them valuable for the conservation of genetic diversity.

  • 39. 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).

  • 40. Eidesen, P. B.
    et al.
    Alsos, I. G.
    Popp, M.
    Stensrud, O.
    Suda, J.
    Brochmann, C.
    Nuclear vs. plastid data: complex Pleistocene history of a circumpolar key species2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 18, p. 3902-3925Article in journal (Refereed)
    Abstract [en]

    To fully understand the contemporary genetic structure of plants, both nuclear and plastid markers are needed. Three chloroplast DNA (cpDNA) lineages, which probably diverged before the major Pleistocene glaciations, have been identified in the circumpolar/circumboreal Vaccinium uliginosum. Here we investigate its nuclear DNA variation using nuclear ribosomal internal transcribed spacer (ITS) sequences, DNA ploidy level measurements and amplified fragment length polymorphisms (AFLPs). We also extend the cpDNA dataset. Two ITS lineages, corresponding to diploids and tetraploids, respectively, were identified. However, both main sequence types apparently occurred in most individual plants but showed ploidy-biased homogenization and possibly reflect paralogy predating the origin of V. uliginosum. The ploidy levels were largely consistent with the cpDNA lineages, suggesting that the initial cpDNA divergence followed early polyploidizations. Five main AFLP groups were identified, consistent with recent glacial refugia in Beringia, western Siberia, the southern European mountains and areas south/east of the Scandinavian and Laurentide ice sheets. Except from the southern European mountains, there has been extensive expansion from all refugia, resulting in several contact zones. Surprisingly, the presumably older ploidy and cpDNA patterns were partly inconsistent with the main AFLP groups and more consistent with AFLP subgroups. A likely major driver causing the inconsistencies is recent nuclear gene flow via unreduced pollen from diploids to tetraploids. This may prevent cytoplasmic introgression and result in overlayed patterns formed by processes dominating at different time scales. The data also suggest more recent polyploidizations, as well as several chloroplast capture events, further complicating this scenario. This study highlights the importance of combining different marker systems to unravel intraspecific histories.

  • 41. Ekblom, Robert
    et al.
    Saether, Stein Are
    Grahn, Mats
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Fiske, Peder
    Kålås, John Atle
    Höglund, Jacob
    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.

  • 42. Ekblom, Robert
    et al.
    Saether, Stein Are
    Jacobsson, Pär
    Fiske, Peder
    Sahlman, Tobias
    Grahn, Mats
    Södertörn University, School of Life Sciences.
    Kålås, John Atle
    Höglund, Jacob
    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.

  • 43.
    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.

  • 44.
    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.

  • 45.
    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.

  • 46.
    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.

  • 47.
    Eroukhmanoff, Fabrice
    et al.
    Section for Animal Ecology, Ecology Building, Lund University, Lund, Sweden.
    Hargeby, Anders
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Svensson, Erik I
    Section for Animal Ecology, Ecology Building, Lund University, Lund, Sweden.
    Rapid adaptive divergence between ecotypes of an aquatic isopod inferred from F-ST-Q(ST) analysis2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, no 23, p. 4912-4923Article in journal (Refereed)
    Abstract [en]

    Divergent natural selection is often thought to be the principal factor driving phenotypic differentiation between populations. We studied two ecotypes of the aquatic isopod Asellus aquaticus which have diverged in parallel in several Swedish lakes. In these lakes, isopods from reed belts along the shores colonized new stonewort stands in the centre of the lakes and rapid phenotypic changes in size and pigmentation followed after colonization. We investigated if selection was likely to be responsible for these observed phenotypic changes using indirect inferences of selection (F-ST-Q(ST) analysis). Average Q(ST) for seven quantitative traits were higher than the average F-ST between ecotypes for putatively neutral markers (AFLPs). This suggests that divergent natural selection has played an important role during this rapid diversification. In contrast, the average Q(ST) between the different reed ecotype populations was not significantly different from the mean F-ST. Genetic drift could therefore not be excluded as an explanation for the minor differences between allopatric populations inhabiting the same source habitat. We complemented this traditional F-ST-Q(ST) approach by comparing the F-ST distributions across all loci (n = 67-71) with the Q(ST) for each of the seven traits. This analysis revealed that pigmentation traits had diverged to a greater extent and at higher evolutionary rates than size-related morphological traits. In conclusion, this extended and detailed type of F-ST-Q(ST) analysis provides a powerful method to infer adaptive phenotypic divergence between populations. However, indirect inferences about the operation of divergent selection should be analyzed on a per-trait basis and complemented with detailed ecological information.

  • 48. 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.

  • 49. 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.

  • 50.
    Forsman, Anders
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Is colour polymorphism advantageous to populations and species?2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 12, p. 2693-2698Article, review/survey (Refereed)
    Abstract [en]

    I am writing in response to an article by Bolton, Rollinsand Griffith (2015) entitled ‘The danger within: the roleof genetic, behavioural and ecological factors in populationpersistence of colour polymorphic species’ that wasrecently published as an Opinion under the NEWS ANDVIEWS section in Molecular Ecology. Bolton et al.(Molecular Ecology, 2015, 24, 2907) argue that colour polymorphismmay reduce population fitness and increaseextinction risk and emphasize that this is contrary to predictionsput forward by Forsman et al. (Ecology, 89, 2008,34) and Wennersten & Forsman (Biological Reviews 87,2012, 756) that the existence of multiple colour morphswith co-adapted gene complexes and associated trait valuesmay increase the ecological and evolutionary successof polymorphic populations and species. Bolton et al.(Molecular Ecology, 2015, 24, 2907) further state that thereis no clear evidence from studies of ‘true polymorphicspecies’ that polymorphism promotes population persistence.In response, I (i) challenge their classifications ofpolymorphisms and revisit the traditional definitions recognizingthe dynamic nature of polymorphisms, (ii)review empirical studies that have examined whetherand how polymorphism is associated with extinction risk,(iii) discuss the roles of trait correlations between colourpattern and other phenotypic dimensions for populationfitness and (iv) highlight that the causes and mechanismsthat influence the composition and maintenance of polymorphismsare different from the consequences of thepolymorphic condition and how it may impact on aspectsof ecological success and long-term persistence of populationsand species.

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