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  • 1. Abbott, R.
    et al.
    Albach, D.
    Ansell, S.
    Arntzen, J. W.
    Baird, S. J. E.
    Bierne, N.
    Boughman, J.
    Brelsford, A.
    Buerkle, C. A.
    Buggs, R.
    Butlin, R. K.
    Dieckmann, U.
    Eroukhmanoff, F.
    Grill, A.
    Cahan, S. H.
    Hermansen, J. S.
    Hewitt, G.
    Hudson, A. G.
    Jiggins, C.
    Jones, J.
    Keller, B.
    Marczewski, T.
    Mallet, J.
    Martinez-Rodriguez, P.
    Möst, M.
    Mullen, S.
    Nichols, R.
    Nolte, A. W.
    Parisod, C.
    Pfennig, K.
    Rice, A. M.
    Ritchie, M. G.
    Seifert, B.
    Smadja, C. M.
    Stelkens, R.
    Szymura, J. M.
    Väinölä, R.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zinner, D.
    Hybridization and speciation2013In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 26, no 2, p. 229-246Article, review/survey (Refereed)
    Abstract [en]

    Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization.

  • 2.
    Camus, M. Florencia
    et al.
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Morrow, Edward H.
    Univ Sussex, Sch Life Sci, Brighton BN1 9QG, E Sussex, England..
    Dowling, Damian K.
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia..
    Single Nucleotides in the mtDNA Sequence Modify Mitochondrial Molecular Function and Are Associated with Sex-Specific Effects on Fertility and Aging2015In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, no 20, p. 2717-2722Article in journal (Refereed)
    Abstract [en]

    Mitochondria underpin energy conversion in eukaryotes. Their small genomes have been the subject of increasing attention, and there is evidence that mitochondrial genetic variation can affect evolutionary trajectories and shape the expression of life-history traits considered to be key human health indicators [1, 2]. However, it is not understood how genetic variation across a diminutive genome, which in most species harbors only about a dozen protein-coding genes, can exert broad-scale effects on the organisnnal phenotype [2, 3]. Such effects are particularly puzzling given that the mitochondrial genes involved are under strong evolutionary constraint and that mitochondrial gene expression is highly conserved across diverse taxa [4]. We used replicated genetic lines in the fruit fly, Drosophila melanogaster, each characterized by a distinct and naturally occurring mitochondrial haplotype placed alongside an isogenic nuclear background. We demonstrate that sequence variation within the mitochondria! DNA (mtDNA) affects both the copy number of mitochondrial genomes and patterns of gene expression across key mitochondrial protein-coding genes. In several cases, haplotype-mediated patterns of gene expression were gene-specific, even for genes from within the same transcriptional units. This invokes post-transcriptional processing of RNA in the regulation of mitochondrial genetic effects on organismal phenotypes. Notably, the haplotype-mediated effects on gene expression could be traced backward to the level of individual nucleotides and forward to sex-specific effects on fertility and longevity. Our study thus elucidates how small-scale sequence changes in the mitochondrial genome can achieve broad-scale regulation of health-related phenotypes and even contribute to sex-related differences in longevity.

  • 3.
    Dutoit, Ludovic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Michigan, Dept Ecol & Evolutionary Biol, Lab Mol & Genom Evolut, Ann Arbor, MI USA..
    Mugal, Carina F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bossu, Christen M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Stockholm Univ, Dept Zool, S-10691 Stockholm, Sweden.
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Friedrich Schiller Univ, Inst Ecol, Dept Ecol, Dornburger Str 159 07743 Jena, Jena, Germany.
    Wolf, Jochen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol 2, Div Evolutionary Biol, Grosshaderner Str 2, D-82152 Martinsried, Germany..
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1849, article id 20162756Article in journal (Refereed)
    Abstract [en]

    Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird speciescollared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's rho = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.

  • 4. Eccard, Jana A.
    et al.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Effects of brood size on multiple-paternity rates: a case for ‘paternity share’ as an offspring-based estimate2009In: Animal Behaviour, ISSN 0003-3472, E-ISSN 1095-8282, Vol. 78, no 2, p. 563-571Article in journal (Refereed)
  • 5.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A field guide to whole-genome sequencing, assembly and annotation2014In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 7, no 9, p. 1026-1042Article in journal (Refereed)
    Abstract [en]

    Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.

  • 6.
    Ellegren, Hans
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Smeds, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ólason, Páll I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kawakami, Takeshi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Künstner, Axel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mäkinen, Hannu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nadachowska-Brzyska, Krystyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Uebbing, Severin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The genomic landscape of species divergence in Ficedula flycatchers2012In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 491, no 7426, p. 756-760Article in journal (Refereed)
    Abstract [en]

    Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre-as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.

  • 7.
    Ellegren, Hans
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany..
    Parallelism in genomic landscapes of differentiation, conserved genomic features and the role of linked selection2017In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, no 8, p. 1516-1518Article in journal (Other academic)
  • 8.
    Foote, Andrew D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Liu, Yue
    Thomas, Gregg W. C.
    Vinar, Tomas
    Alfoeldi, Jessica
    Deng, Jixin
    Dugan, Shannon
    van Elk, Cornelis E.
    Hunter, Margaret E.
    Joshi, Vandita
    Khan, Ziad
    Kovar, Christie
    Lee, Sandra L.
    Lindblad-Toh, Kerstin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Mancia, Annalaura
    Nielsen, Rasmus
    Qin, Xiang
    Qu, Jiaxin
    Raney, Brian J.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hahn, Matthew W.
    Muzny, Donna M.
    Worley, Kim C.
    Gilbert, M. Thomas P.
    Gibbs, Richard A.
    Convergent evolution of the genomes of marine mammals2015In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 47, no 3, p. 272-275Article in journal (Refereed)
    Abstract [en]

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

  • 9.
    Foote, Andrew D.
    et al.
    Univ Bern, Inst Ecol & Evolut, CMPG, Baltzerstr 6, CH-3012 Bern, Switzerland.
    Martin, Michael D.
    NTNU Univ Museum, Trondheim, Norway.
    Louis, Marie
    Univ Copenhagen, Dept Biol, Sect Evolutionary Genom, Copenhagen, Denmark;Univ St Andrews, East Sands, Scottish Oceans Inst, St Andrews, Fife, Scotland.
    Pacheco, George
    Univ Copenhagen, Dept Biol, Sect Evolutionary Genom, Copenhagen, Denmark.
    Robertson, Kelly M.
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Sinding, Mikkel-Holger S.
    Univ Copenhagen, Dept Biol, Sect Evolutionary Genom, Copenhagen, Denmark;Greenland Inst Nat Resources, Nuuk, Greenland.
    Amaral, Ana R.
    Amer Museum Nat Hist, New York, NY 10024 USA;Univ Lisbon, Fac Ciencias, Ctr Ecol Evolut & Environm Changes, Lisbon, Portugal.
    Baird, Robin W.
    Cascadia Res, Olympia, WA USA.
    Baker, Charles Scott
    Oregon State Univ, Marine Mammal Inst, Dept Fisheries & Wildlife, Newport, OR USA;Univ Auckland, Sch Biol Sci, Auckland, New Zealand.
    Ballance, Lisa
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Barlow, Jay
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Brownlow, Andrew
    SRUC Vet Serv Drummondhill, Scottish Marine Anim Stranding Scheme, Inverness, Scotland.
    Collins, Tim
    Wildlife Conservat Soc, Ocean Giants Program, New York, NY USA.
    Constantine, Rochelle
    Univ Auckland, Sch Biol Sci, Auckland, New Zealand.
    Dabin, Willy
    Univ La Rochelle, CNRS, Observ Pelagis, La Rochelle, France.
    Dalla Rosa, Luciano
    Univ Fed Rio Grande, Inst Oceanog, Lab Ecol & Conservacao Megafauna Marinha, Rio Grande, Brazil.
    Davison, Nicholas J.
    SRUC Vet Serv Drummondhill, Scottish Marine Anim Stranding Scheme, Inverness, Scotland.
    Durban, John W.
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Esteban, Ruth
    CIRCE Conservat Informat & Res Cetaceans, Algeciras, Spain.
    Ferguson, Steven H.
    Fisheries & Oceans Canada, Winnipeg, MB, Canada.
    Gerrodette, Tim
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Guinet, Christophe
    CNRS ULR, CEBC, UMR, Chize, France.
    Hanson, M. Bradley
    NOAA, Natl Marine Fisheries Serv, Northwest Fisheries Sci Ctr, Seattle, WA 98115 USA.
    Hoggard, Wayne
    NOAA, Natl Marine Fisheries Serv, Southeast Fisheries Sci Ctr, Pascagoula, MS USA.
    Matthews, Cory J. D.
    Fisheries & Oceans Canada, Winnipeg, MB, Canada.
    Samarra, Filipa I. P.
    Marine & Freshwater Res Inst, Reykjavik, Iceland.
    de Stephanis, Renaud
    CIRCE Conservat Informat & Res Cetaceans, Algeciras, Spain.
    Tavares, Sara B.
    Univ St Andrews, East Sands, Scottish Oceans Inst, St Andrews, Fife, Scotland.
    Tixier, Paul
    CNRS ULR, CEBC, UMR, Chize, France;Deakin Univ, Sch Life & Environm Sci, Burwood Campus, Geelong, Vic, Australia.
    Totterdell, John A.
    Marine Informat & Res Grp Australia MIRG, Quinns Rocks, WA, Australia.
    Wade, Paul
    NOAA, Natl Marine Mammal Lab, Natl Marine Fisheries Serv, Alaska Fisheries Sci Ctr, Washington, DC USA.
    Excoffier, Laurent
    Univ Bern, Inst Ecol & Evolut, CMPG, Baltzerstr 6, CH-3012 Bern, Switzerland.
    Gilbert, M. Thomas P.
    NTNU Univ Museum, Trondheim, Norway;Univ Copenhagen, Dept Biol, Sect Evolutionary Genom, Copenhagen, Denmark.
    Wolf, Jochen B. W.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany.
    Morin, Phillip A.
    NOAA, Marine Mammal & Turtle Div, Natl Marine Fisheries Serv, Southwest Fisheries Sci Ctr, La Jolla, CA USA.
    Killer whale genomes reveal a complex history of recurrent admixture and vicariance2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 14, p. 3427-3444Article in journal (Refereed)
    Abstract [en]

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

  • 10.
    Foote, Andrew D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Volgade 5-7, DK-1350 Copenhagen K, Denmark.;Univ Bern, Inst Ecol & Evolut, Computat & Mol Populat Genet Lab, Baltzerstr 6, CH-3012 Bern, Switzerland..
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Avila-Arcos, Maria C.
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Volgade 5-7, DK-1350 Copenhagen K, Denmark.;Stanford Univ, Dept Genet, Stanford, CA 94305 USA..
    Baird, Robin W.
    Cascadia Res, 4th Ave, Olympia, WA 98501 USA..
    Durban, John W.
    NOAA, Marine Mammal & Turtle Div, Southwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, 8901 La Jolla Shores Dr, La Jolla, CA 92037 USA..
    Fumagalli, Matteo
    UCL, UCL Genet Inst, Dept Genet Evolut & Environm, London WC1E 6BT, England..
    Gibbs, Richard A.
    Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, One Baylor Plaza, Houston, TX 77030 USA..
    Hanson, M. Bradley
    NOAA, NW Fisheries Sci Ctr, Natl Marine Fisheries Serv, 2725 Montlake Blvd East, Seattle, WA 98112 USA..
    Korneliussen, Thorfinn S.
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Volgade 5-7, DK-1350 Copenhagen K, Denmark..
    Martin, Michael D.
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Volgade 5-7, DK-1350 Copenhagen K, Denmark..
    Robertson, Kelly M.
    NOAA, Marine Mammal & Turtle Div, Southwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, 8901 La Jolla Shores Dr, La Jolla, CA 92037 USA..
    Sousa, Vitor C.
    Univ Bern, Inst Ecol & Evolut, Computat & Mol Populat Genet Lab, Baltzerstr 6, CH-3012 Bern, Switzerland..
    Vieira, Filipe G.
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Volgade 5-7, DK-1350 Copenhagen K, Denmark..
    Vinar, Tomas
    Comenius Univ, Fac Math Phys & Informat, Bratislava 84248, Slovakia..
    Wade, Paul
    NOAA, Natl Marine Mammal Lab, Alaska Fisheries Sci Ctr, Natl Marine Fisheries Serv, 7600 Sand Point Way NE, Seattle, WA 98115 USA..
    Worley, Kim C.
    Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, One Baylor Plaza, Houston, TX 77030 USA..
    Excoffier, Laurent
    Univ Bern, Inst Ecol & Evolut, Computat & Mol Populat Genet Lab, Baltzerstr 6, CH-3012 Bern, Switzerland..
    Morin, Phillip A.
    NOAA, Marine Mammal & Turtle Div, Southwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, 8901 La Jolla Shores Dr, La Jolla, CA 92037 USA..
    Gilbert, M. Thomas P.
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Volgade 5-7, DK-1350 Copenhagen K, Denmark.;Curtin Univ, Dept Environm & Agr, Trace & Environm DNA Lab, Perth, WA 6102, Australia..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Munich, Dept Biol 2, Sect Evolutionary Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany..
    Genome-culture coevolution promotes rapid divergence of killer whale ecotypes2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11693Article in journal (Refereed)
    Abstract [en]

    Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.

  • 11.
    Grosser, Stefanie
    et al.
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany;Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany.
    Sauer, Jan
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany.
    Paijmans, Anneke J.
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany.
    Caspers, Barbara A.
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany.
    Forcada, Jaume
    NERC, British Antarctic Survey, Cambridge, England.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany.
    Hoffman, Joseph I.
    Bielefeld Univ, Dept Anim Behav, Bielefeld, Germany;NERC, British Antarctic Survey, Cambridge, England.
    Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 9, p. 2406-2422Article in journal (Refereed)
    Abstract [en]

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

  • 12.
    Hooper, Rebecca
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Brealey, Jaelle C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    van der Valk, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Alberdi, Antton
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.
    Durban, John W
    Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California.
    Fearnbach, Holly
    SR3, SeaLife Response, Rehabilitation, and Research, Seattle, Washington.
    Robertson, Kelly M
    Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California.
    Baird, Robin W
    Cascadia Research, Olympia, Washington.
    Hanson, M. Bradley
    Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington.
    Wade, Paul
    National Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington.
    Gilbert, M Thomas P
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark ; NTNU University Museum, Trondheim, Norway.
    Morin, Phillip A
    Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Section of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany.
    Foote, Andrew D
    Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK.
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 2, p. 484-502Article in journal (Refereed)
    Abstract [en]

    Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.

  • 13.
    Humble, Emily
    et al.
    Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.;British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England..
    Dasmahapatra, Kanchon K.
    Univ York, Dept Biol, York YO10 5DD, N Yorkshire, England..
    Martínez Barrio, Álvaro
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Gregorio, Ines
    Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany..
    Forcada, Jaume
    British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England..
    Polikeit, Ann-Christin
    Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany..
    Goldsworthy, Simon D.
    South Australian Res & Dev Inst, 2 Hamra Ave, West Beach, SA 5024, Australia..
    Goebel, Michael E.
    NOAA, Antarctic Ecosyst Res Div, SWFSC, NMFS, La Jolla, CA 92037 USA..
    Kalinowski, Jorn
    Univ Bielefeld, CeBiTec, Ctr Biotechnol, Univ Str 27, D-33615 Bielefeld, Germany..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinstried, Germany..
    Hoffman, Joseph, I
    Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.;British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England..
    RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding2018In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 8, p. 2709-2722Article in journal (Refereed)
    Abstract [en]

    Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.

  • 14.
    Jeglinski, Jana W. E.
    et al.
    Univ Glasgow, Inst Biodivers Anim Hlth & Comparat Med, Glasgow, Lanark, Scotland.;Univ Bielefeld, Anim Behav, D-33615 Bielefeld, Germany..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Werner, Christiane
    Univ Bayreuth, BAYCEER, Dept Agroecosyst Res, Bayreuth, Germany.;Univ Freiburg, Dept Ecosyst Physiol, Freiburg Im Breisgau, Germany..
    Costa, Daniel P.
    Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA..
    Trillmich, Fritz
    Univ Bielefeld, Anim Behav, D-33615 Bielefeld, Germany..
    Differences in foraging ecology align with genetically divergent ecotypes of a highly mobile marine top predator2015In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 179, no 4, p. 1041-1052Article in journal (Refereed)
    Abstract [en]

    Foraging differentiation within a species can contribute to restricted gene flow between ecologically different groups, promoting ecological speciation. Galapagos sea lions (Zalophus wollebaeki) show genetic and morphological divergence between the western and central archipelago, possibly as a result of an ecologically mediated contrast in the marine habitat. We use global positioning system (GPS) data, time-depth recordings (TDR), stable isotope and scat data to compare foraging habitat characteristics, diving behaviour and diet composition of Galapagos sea lions from a western and a central colony. We consider both juvenile and adult life stages to assess the potential role of ontogenetic shifts that can be crucial in shaping foraging behaviour and habitat choice for life. We found differences in foraging habitat use, foraging style and diet composition that aligned with genetic differentiation. These differences were consistent between juvenile and adult sea lions from the same colony, overriding age-specific behavioural differences. Our study contributes to an understanding of the complex interaction of ecological condition, plastic behavioural response and genetic make-up of interconnected populations.

  • 15.
    Knief, Ulrich
    et al.
    Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Munich, Germany.
    Bossu, Christen M.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Stockholm Univ, Dept Zool, Populat Genet, Stockholm, Sweden;Univ Calif Los Angeles, Ctr Trop Res, Inst Environm & Sustainabil, Los Angeles, CA USA.
    Saino, Nicola
    Univ Milan, Dept Environm Sci & Policy, Milan, Italy.
    Hansson, Bengt
    Lund Univ, Dept Biol, Lund, Sweden.
    Poelstra, Jelmer
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Duke Univ, Biol Dept, Durham, NC USA.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Indian Inst Sci Educ & Res, Dept Biol Sci, Bhopal, India.
    Weissensteiner, Matthias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Munich, Germany.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Munich, Germany.
    Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone2019In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, no 4, p. 570-576Article in journal (Refereed)
    Abstract [en]

    The evolution of genetic barriers opposing interspecific gene flow is key to the origin of new species. Drawing from information on over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a similar to 2.8-megabase region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.

  • 16. Krueger, Oliver
    et al.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jonker, Rudy M.
    Hoffman, Joseph I.
    Trillmich, Fritz
    Disentangling the Contribution of Sexual Selection and Ecology to the Evolution of Size Dimorphism in Pinnipeds2014In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, no 5, p. 1485-1496Article in journal (Refereed)
    Abstract [en]

    The positive relationship between sexual size dimorphism (SSD) and harem size across pinnipeds is often cited as a textbook example of sexual selection. It assumes that female aggregation selected for large male size via male–male competition. Yet, it is also conceivable that SSD evolved prior to polygyny due to ecological forces. We analyzed 11 life-history traits in 35 pinniped species to determine their coevolutionary dynamics and infer their most likely evolutionary trajectories contrasting these two hypotheses. We find support for SSD having evolved prior to changes in the mating system, either as a consequence of niche partitioning during aquatic foraging or in combination with sexual selection on males to enforce copulations on females. Only subsequently did polygyny evolve, leading to further coevolution as the strength of sexual selection intensified. Evolutionary sequence analyses suggest a polar origin of pinnipeds and indicate that SSD and polygyny are intrinsically linked to a suite of ecological and life-history traits. Overall, this study calls for the inclusion of ecological variables when studying sexual selection and argues for caution when assuming causality between coevolving traits. It provides novel insights into the role of sexual selection for the coevolutionary dynamics of SSD and mating system.

  • 17.
    Künstner, Axel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whitney, Osceola
    Balakrishnan, Christopher N.
    Day, Lainy
    Edwards, Scott V.
    Janes, Daniel E.
    Schlinger, Barney A.
    Wilson, Richard K.
    Jarvis, Erich D.
    Warren, Wesley C.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no Suppl.1, p. 266-276Article in journal (Refereed)
    Abstract [en]

    Next-generation sequencing technology provides an attractive means to obtain largescale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with ∼1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (dS) and chromosome size. Analyses of the mean dN/dS ratio (ω) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with x as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.

  • 18. Lenz, Tobias L.
    et al.
    Mueller, Birte
    Trillmich, Fritz
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Divergent allele advantage at MHC-DRB through direct and maternal genotypic effects and its consequences for allele pool composition and mating2013In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 280, no 1762, p. 20130714-Article in journal (Refereed)
    Abstract [en]

    It is still debated whether main individual fitness differences in natural populations can be attributed to genome-wide effects or to particular loci of outstanding functional importance such as the major histocompatibility complex (MHC). In a long-term monitoring project on Galapagos sea lions (Zalophus wollebaeki), we collected comprehensive fitness and mating data for a total of 506 individuals. Controlling for genome-wide inbreeding, we find strong associations between the MHC locus and nearly all fitness traits. The effect was mainly attributable to MHC sequence divergence and could be decomposed into contributions of own and maternal genotypes. In consequence, the population seems to have evolved a pool of highly divergent alleles conveying near-optimal MHC divergence even by random mating. Our results demonstrate that a single locus can significantly contribute to fitness in the wild and provide conclusive evidence for the 'divergent allele advantage' hypothesis, a special form of balancing selection with interesting evolutionary implications.

  • 19.
    Lopes, Fernando
    et al.
    Univ Vale Rio dos Sinos UNISINOS, BR-93022000 Sao Leopoldo, RS, Brazil.;Pontificia Univ Catolica Rio Grande sul PUCRS, BR-90619900 Porto Alegre, RS, Brazil..
    Hoffman, Joseph Ivan
    Univ Bielefeld, D-33501 Bielefeld, Germany..
    Valiati, Victor Hugo
    Univ Vale Rio dos Sinos UNISINOS, BR-93022000 Sao Leopoldo, RS, Brazil..
    Bonatto, Sandro L.
    Pontificia Univ Catolica Rio Grande sul PUCRS, BR-90619900 Porto Alegre, RS, Brazil..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Trillmich, Fritz
    Univ Bielefeld, D-33501 Bielefeld, Germany..
    Oliveira, Larissa R.
    Univ Vale Rio dos Sinos UNISINOS, BR-93022000 Sao Leopoldo, RS, Brazil.;Grp Estudos Mamiferos Aquaticos Rio Grande Sul GE, BR-95625000 Imbe, RS, Brazil..
    Fine-scale matrilineal population structure in the Galapagos fur seal and its implications for conservation management2015In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 16, no 5, p. 1099-1113Article in journal (Refereed)
    Abstract [en]

    Females of many pinniped species generally exhibit strong fine-scale philopatry, but it is unclear over what spatial scale this behavior may translate into genetic population structure. We conducted a population genetic survey in the Galapagos fur seal, Arctocephalus galapagoensis, an endangered pinniped endemic to a small geographic range in the northwest of the Galapagos archipelago. To assess patterns of genetic diversity levels and population differentiation, we analyzed part of the mitochondrial control region (mtDNA) and 18 microsatellites DNA markers. We detected similar levels of genetic diversity to many other pinniped species (h = 0.86, pi = 0.012, A = 7.44) despite severe anthropogenic exploitation in the nineteenth century and recurrent population crashes due to recent climatic perturbations associated with El Nio Southern Oscillation events. We further found remarkably strong fine-scale matrilineal population structure, with 33.9 % of the mtDNA variation being partitioned among colonies separated by as little as 70 km swimming distance. In contrast, population structure inferred from nuclear markers was weak. Our findings provide further evidence that natal philopatry can translate into fine-scale genetic population structure in highly mobile species. We discuss the relevance of our results for the fine-scale conservation management of this species with a very restricted geographic range.

  • 20. Mueller, Birte
    et al.
    Pörschmann, Ulrich
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Trillmich, Fritz
    Growth under uncertainty: The influence of marine variability on early development of Galapagos sea lions2011In: Marine mammal science, ISSN 0824-0469, E-ISSN 1748-7692, Vol. 27, no 2, p. 350-365Article in journal (Refereed)
    Abstract [en]

    Abstract Development implies a change in allocation of resources from somatic growth to reproduction. In a highly variable environment, growth can vary from year to year thereby influencing the long-term life history perspective. The Galapagos sea lion (Zalophus wollebaeki) lives in a highly unpredictable marine environment in which food abundance varies not only seasonally, but also annually due to El Niño. Galapagos sea lions are restricted to a patch of cold upwelling waters surrounding the archipelago and are closely tied to land as nursing females alternate between foraging at sea and nursing ashore. Therefore, their offspring are especially vulnerable to ocean warming causing reduced food abundance. We found a significant correlation between sea surface temperature (SST) and early growth: Both mass at birth and linear growth within the first 2 mo of life correlated negatively with SST. Absolute mass gain was higher for males, but both sexes gained equally 1.9% of birth mass per day. Until the age of 3 yr male and female juveniles showed similar growth to an asymptotic mass of 40 and 35 kg, respectively. As a consequence of the highly variable environment, the plasticity in growth strategy of Galapagos sea lion juveniles appears wider than that of all other sea lions allowing them to cope with poor conditions.

  • 21.
    Mugal, Carina F
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B W
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kaj, Ingemar
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS2014In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 1, p. 212-231Article in journal (Refereed)
    Abstract [en]

    The ratio of divergence at nonsynonymous and synonymous sites, dN/dS, is a widely used measure in evolutionary genetic studies to investigate the extent to which selection modulates gene sequence evolution. Originally tailored to codon sequences of distantly related lineages, dN/dS represents the ratio of fixed nonsynonymous to synonymous differences. The impact of ancestral and lineage-specific polymorphisms on dN/dS, which we here show to be substantial for closely related lineages, is generally neglected in estimation techniques of dN/dS. To address this issue, we formulate a codon model that is firmly anchored in population genetic theory, derive analytical expressions for the dN/dS measure by Poisson random field approximation in a Markovian framework and validate the derivations by simulations. In good agreement, simulations and analytical derivations demonstrate that dN/dS is biased by polymorphisms at short time scales and that it can take substantial time for the expected value to settle at its time limit where only fixed differences are considered. We further show that in any attempt to estimate the dN/dS ratio from empirical data the effect of the intrinsic fluctuations of a ratio of stochastic variables, can even under neutrality yield extreme values of dN/dS at short time scales or in regions of low mutation rate. Taken together, our results have significant implications for the interpretation of dN/dS estimates, the McDonald-Kreitman test and other related statistics, in particular for closely related lineages.

  • 22.
    Mugal, Carina F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    von Gruenberg, H. H.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes2010In: Genome Biology and Evolution, ISSN 1759-6653, Vol. 2, no 1, p. 19-28Article in journal (Refereed)
    Abstract [en]

    Local variation in neutral substitution rate across mammalian genomes is governed by several factors, including sequence context variables and structural variables. In addition, the interplay of replication and transcription, known to induce a strand bias in mutation rate, gives rise to variation in substitutional strand asymmetries. Here, we address the conservation of variation in mutation rate and substitutional strand asymmetries using primate-and rodent-specific repeat elements located within the introns of protein-coding genes. We find significant but weak conservation of local mutation rates between human and mouse orthologs. Likewise, substitutional strand asymmetries are conserved between human and mouse, where substitution rate asymmetries show a higher degree of conservation than mutation rate. Moreover, we provide evidence that replication and transcription are correlated to the strength of substitutional asymmetries. The effect of transcription is particularly visible for genes with highly conserved gene expression. In comparison with replication and transcription, mutation rate influences the strength of substitutional asymmetries only marginally.

  • 23.
    Nabholz, Benoit
    et al.
    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.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    High Levels of Gene Expression Explain the Strong Evolutionary Constraint of Mitochondrial Protein-Coding Genes2013In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 30, no 2, p. 272-284Article in journal (Refereed)
    Abstract [en]

    The nearly neutral theory of molecular evolution has been widely accepted as the guiding principle for understanding how selection affects gene sequence evolution. One of its central predictions is that the rate at which proteins evolve should negatively scale with effective population size (N-e). In contrast to the expectation of reduced selective constraint in the mitochondrial genome following from its lower N-e, we observe what can be interpreted as the opposite: for a taxonomically diverse set of organisms (birds, mammals, insects, and nematodes), mitochondrially encoded protein-coding genes from the oxidative phosphorylation pathway (mtOXPHOS; n = 12-13) show markedly stronger signatures of purifying selection (illustrated by low d(N)/d(S)) than their nuclear counterparts interacting in the same pathway (nuOXPHOS; n: similar to 75). To understand these unexpected evolutionary dynamics, we consider a number of structural and functional parameters including gene expression, hydrophobicity, transmembrane position, gene ontology, GC content, substitution rate, proportion of amino acids in transmembrane helices, and protein-protein interaction. Across all taxa, unexpectedly large differences in gene expression levels (RNA-seq) between nuclear and mitochondrially encoded genes, and to a lower extent hydrophobicity, explained most of the variation in d(N)/d(S). Similarly, differences in d(N)/d(S) between functional OXPHOS protein complexes could largely be explained by gene expression differences. Overall, by including gene expression and other functional parameters, the unexpected mitochondrial evolutionary dynamics can be understood. Our results not only reaffirm the link between gene expression and protein evolution but also open new questions about the functional role of expression level variation between mitochondrial genes.

  • 24.
    Nam, Kiwoong
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nabholz, Benoit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schielzeth, Holger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Künstner, Axel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Balakrishnan, Christopher N.
    Heger, Andreas
    Ponting, Chris P.
    Clayton, David F.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Molecular evolution of genes in avian genomes2010In: Genome Biology, ISSN 1474-760X, Vol. 11, no 6, p. R68-Article in journal (Refereed)
    Abstract [en]

    Background: Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1: 1 orthologs of chicken, zebra finch, a lizard and three mammalian species. Results: We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an over-representation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton. Conclusions: Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between omega and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes.

  • 25.
    Nieuwenhuis, Bart P. S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany.
    Tusso Gomez, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany.
    Bjerling, Pernilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stångberg, Josefine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany.
    Immler, Simone
    Uppsala Univ, Dept Evolutionary Biol, SE-75236 Uppsala, Sweden;Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.
    Repeated evolution of self-compatibility for reproductive assurance2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 1639Article in journal (Refereed)
    Abstract [en]

    Sexual reproduction in eukaryotes requires the fusion of two compatible gametes of opposite sexes or mating types. To meet the challenge of finding a mating partner with compatible gametes, evolutionary mechanisms such as hermaphroditism and self-fertilization have repeatedly evolved. Here, by combining the insights from comparative genomics, computer simulations and experimental evolution in fission yeast, we shed light on the conditions promoting separate mating types or self-compatibility by mating-type switching. Analogous to multiple independent transitions between switchers and non-switchers in natural populations mediated by structural genomic changes, novel switching genotypes readily evolved under selection in the experimental populations. Detailed fitness measurements accompanied by computer simulations show the benefits and costs of switching during sexual and asexual reproduction, governing the occurrence of both strategies in nature. Our findings illuminate the trade-off between the benefits of reproductive assurance and its fitness costs under benign conditions facilitating the evolution of self-compatibility.

  • 26.
    Poelstra, Jelmer W.
    et al.
    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.
    Wolf, Jochen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone2013In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 111, no 6, p. 467-473Article in journal (Refereed)
    Abstract [en]

    Colouration patterns have an important role in adaptation and speciation. The European crow system, in which all-black carrion crows and grey-coated hooded crows meet in a narrow hybrid zone, is a prominent example. The marked phenotypic difference is maintained by assortative mating in the absence of neutral genetic divergence, suggesting the presence of few pigmentation genes of major effect. We made use of the rich phenotypic and genetic resources in mammals and identified a comprehensive panel of 95 candidate pigmentation genes for birds. Based on functional annotation, we chose a subset of the most promising 37 candidates, for which we developed a marker system that demonstrably works across the avian phylogeny. In total, we sequenced 107 amplicons (~3 loci per gene, totalling 60 kb) in population samples of crows (n=23 for each taxon). Tajima’s D, Fu’s FS, DHEW and HKA (Hudson–Kreitman–Aguade) statistics revealed several amplicons that deviated from neutrality; however, none of these showed significantly elevated differentiation between the two taxa. Hence, colour divergence in this system may be mediated by uncharacterized pigmentation genes or regulatory regions outside genes. Alternatively, the observed high population recombination rate (4Ner~0.03), with overall linkage disequilibrium dropping rapidly within the order of few 100 bp, may compromise the power to detect causal loci with nearby markers. Our results add to the debate as to the utility of candidate gene approaches in relation to genomic features and the genetic architecture of the phenotypic trait in question.

  • 27.
    Poelstra, Jelmer W.
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bossu, Christen M.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lantz, Henrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ryll, Bettina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Mueller, I.
    Baglione, V.
    Unneberg, P.
    Wikelski, M.
    Grabherr, Manfred G.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Wolf, Jochen B. W.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The genomic landscape underlying phenotypic integrity in the face of gene flow in crows2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, no 6190, p. 1410-1414Article in journal (Refereed)
    Abstract [en]

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

  • 28.
    Poelstra, Jelmer W.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hoeppner, M. P.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Linkopings Univ Victoria Westling, Bioinformat Infrastruct Life Sci, S-58183 Linkoping, Sweden..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Transcriptomics of colour patterning and coloration shifts in crows2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 18, p. 4617-4628Article in journal (Refereed)
    Abstract [en]

    Animal coloration is one of the most conspicuous phenotypic traits in natural populations and has important implications for adaptation and speciation. Changes in coloration can occur over surprisingly short evolutionary timescales, while recurrence of similar colour patterns across large phylogenetic distances is also common. Even though the genetic basis of pigment production is well understood, little is known about the mechanisms regulating colour patterning. In this study, we shed light on the molecular elements regulating regional pigment production in two genetically near-identical crow taxa with striking differences in a eumelanin-based phenotype: black carrion and grey-coated hooded crows. We produced a high-quality genome annotation and analysed transcriptome data from a 2 3 2 design of active melanogenic feather follicles from head (black in both taxa) and torso (black in carrion and grey in hooded crow). Extensive, parallel expression differences between body regions in both taxa, enriched for melanogenesis genes (e.g. ASIP, CORIN, and ALDH6), indicated the presence of cryptic prepatterning also in all-black carrion crows. Meanwhile, colour-specific expression (grey vs. black) was limited to a small number of melanogenesis genes in close association with the central transcription factor MITF (most notably HPGDS, NDP and RASGRF1). We conclude that colour pattern differences between the taxa likely result from an interaction between divergence in upstream elements of the melanogenesis pathway and genes that provide an underlying prepattern across the body through positional information. A model of evolutionary stable prepatterns that can be exposed and masked through simple regulatory changes may explain the phylogenetically independent recurrence of colour patterns that is observed across corvids and many other vertebrate groups.

  • 29. Pörschmann, Ulrich
    et al.
    Trillmich, Fritz
    Mueller, Birte
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Male reproductive success and its behavioural correlates in a polygynous mammal, the Galapagos sea lion (Zalophus wollebaeki)2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 12, p. 2574-2586Article in journal (Refereed)
    Abstract [en]

    Sexual selection theory predicts competitive males and choosy females. Nevertheless, since molecular marker-based studies, paternity outside the expected mating patterns has increasingly been described. Even in highly polygynous systems, where paternity is expected to be strongly skewed towards large, dominant males, alternative mating tactics have been suggested. We examined reproductive success in the polygynous Galapagos sea lion (Zalophus wollebaeki). Semiaquatic territoriality allows females to move freely and may lower the degree of polygyny otherwise suggested by both territorial behaviour and strong sexual dimorphism. We assigned paternities with 22 microsatellites and analysed how male reproductive success was related to size, dominance status, intrasexual agonistic behaviour, proximity to females, and attendance in the colony. Male behaviour was consistent across two seasons for all parameters under consideration. Attendance was by far the most important determinant of paternal success. Skew in reproductive success towards large, dominant males was weak and dominance status played no role. This appears to be caused by an extremely long reproductive season lasting five or more months, making it difficult for any male to monopolize receptive females. Females seem to choose displaying males that were present in the colony for a long time rather than dominance per se. Sexual dimorphism in Galapagos sea lions may thus be more influenced by selection for fasting than fighting ability. Our data provide further evidence for alternative mating tactics, as several males gained relatively high reproductive success despite short attendance and hardly any involvement in agonistic interactions.

  • 30.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gattepaille, Lucie M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Stewart, Robert E. A.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 2, p. 328-345Article in journal (Refereed)
    Abstract [en]

    Approximate Bayesian computation (ABC) is a powerful tool for model-based inference of demographic histories from large genetic data sets. For most organisms, its implementation has been hampered by the lack of sufficient genetic data. Genotyping-by-sequencing (GBS) provides cheap genome-scale data to fill this gap, but its potential has not fully been exploited. Here, we explored power, precision and biases of a coalescent-based ABC approach where GBS data were modelled with either a population mutation parameter () or a fixed site (FS) approach, allowing single or several segregating sites per locus. With simulated data ranging from 500 to 50000 loci, a variety of demographic models could be reliably inferred across a range of timescales and migration scenarios. Posterior estimates were informative with 1000 loci for migration and split time in simple population divergence models. In more complex models, posterior distributions were wide and almost reverted to the uninformative prior even with 50000 loci. ABC parameter estimates, however, were generally more accurate than an alternative composite-likelihood method. Bottleneck scenarios proved particularly difficult, and only recent bottlenecks without recovery could be reliably detected and dated. Notably, minor-allele-frequency filters - usual practice for GBS data - negatively affected nearly all estimates. With this in mind, we used a combination of FS and approaches on empirical GBS data generated from the Atlantic walrus (Odobenus rosmarus rosmarus), collectively providing support for a population split before the last glacial maximum followed by asymmetrical migration and a high Arctic bottleneck. Overall, this study evaluates the potential and limitations of GBS data in an ABC-coalescence framework and proposes a best-practice approach.

  • 31.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Northrup, Joseph M.
    Colorado State Univ, Dept Fish Wildlife & Conservat Biol, Ft Collins, CO 80523 USA..
    Wikelski, Martin
    Max Planck Inst Ornithol, Radolfzell am Bodensee, Germany.;Univ Konstanz, Biol, Constance, Germany..
    Wittemyer, George
    Colorado State Univ, Dept Fish Wildlife & Conservat Biol, Ft Collins, CO 80523 USA..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing2016In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 14, no 1, article id e1002350Article in journal (Refereed)
    Abstract [en]

    Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking the separate data streams from these technologies. Such a merger will elucidate the genetic basis of adaptive behaviors like migration and hibernation and advance our understanding of fundamental ecological and evolutionary processes such as pathogen transmission, population responses to environmental change, and communication in natural populations.

  • 32.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Trent Univ, Forens Sci & Environm & Life Sci, 2014 East Bank Dr, Peterborough, ON K9J 7B8, Canada..
    Peart, Claire R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Tusso, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Maayan, Inbar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Brelsford, Alan
    Univ Lausanne, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Wheat, Christopher W.
    Stockholm Univ, Dept Zool, S-10691 Stockholm, Sweden..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany..
    Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference2017In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, no 8, p. 907-917Article in journal (Refereed)
    Abstract [en]

    1. Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure precise and unbiased interpretation. 2. To test the impact of bioinformatic data processing on downstream population genetic inferences, we analysed mammalian RAD-seq data (>100 individuals) with 312 combinations of methodology (de novo vs. mapping to references of increasing divergence) and filtering criteria (missing data, HWE, F-IS, coverage, mapping and genotype quality). In an effort to identify commonalities and biases in all pipelines, we computed summary statistics (nr. loci, nr. SNP, pi, Het(obs), F-IS, F-ST, N-e and m) and compared the results to independent null expectations (isolation-by-distance correlation, expected transition-to-transversion ratio T-s/T-v and Mendelian mismatch rates of known parent-offspring trios). 3. We observed large differences between reference-based and de novo approaches, the former generally calling more SNPs and reducing F-IS and T-s/T-v. Data completion levels showed little impact on most summary statistics, and FST estimates were robust across all pipelines. The site frequency spectrum was highly sensitive to the chosen approach as reflected in large variance of parameter estimates across demographic scenarios (single-population bottlenecks and isolation-with-migration model). Null expectations were best met by reference-based approaches, although contingent on the specific criteria. 4. We recommend that RAD-seq studies employ reference-based approaches to a closely related genome, and due to the high stochasticity associated with the pipeline advocate the use of multiple pipelines to ensure robust population genetic and demographic inferences.

  • 33.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology2013In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 16, no 7, p. 940-950Article, review/survey (Refereed)
    Abstract [en]

    Ecologically mediated selection has increasingly become recognised as an important driver of speciation. The correlation between neutral genetic differentiation and environmental or phenotypic divergence among populations, to which we collectively refer to as isolation-by-ecology (IBE), is an indicator of ecological speciation. In a meta-analysis framework, we determined the strength and commonality of IBE in nature. On the basis of 106 studies, we calculated a mean effect size of IBE with and without controlling for spatial autocorrelation among populations. Effect sizes were 0.34 (95% CI 0.24-0.42) and 0.26 (95% CI 0.13-0.37), respectively, indicating that an average of 5% of the neutral genetic differentiation among populations was explained purely by ecological contrast. Importantly, spatial autocorrelation reduced IBE correlations for environmental variables, but not for phenotypes. Through simulation, we showed how the influence of isolation-by-distance and spatial autocorrelation of ecological variables can result in false positives or underestimated correlations if not accounted for in the IBE model. Collectively, this meta-analysis showed that ecologically induced genetic divergence is pervasive across time-scales and taxa, and largely independent of the choice of molecular marker. We discuss the importance of these results in the context of adaptation and ecological speciation and suggest future research avenues.

  • 34.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Alves, Paulo C.
    Bergström, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bruford, Michael W.
    Brannstrom, Ioana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Colling, Guy
    Dalen, Love
    De Meester, Luc
    Ekblom, Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Fawcett, Katie D.
    Fior, Simone
    Hajibabaei, Mehrdad
    Hill, Jason A.
    Hoezel, A. Rus
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jensen, Evelyn L.
    Krause, Johannes
    Kristensen, Torsten N.
    Kruetzen, Michael
    McKay, John K.
    Norman, Anita J.
    Ogden, Rob
    Österling, E. Martin
    Ouborg, N. Joop
    Piccolo, John
    Popovic, Danijela
    Primmer, Craig R.
    Reed, Floyd A.
    Roumet, Marie
    Salmona, Jordi
    Schenekar, Tamara
    Schwartz, Michael K.
    Segelbacher, Gernot
    Senn, Helen
    Thaulow, Jens
    Valtonen, Mia
    Veale, Andrew
    Vergeer, Philippine
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vila, Caries
    Weissensteiner, Matthias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wennerstrom, Lovisa
    Wheat, Christopher W.
    Zielinski, Piotr
    Genomics and the challenging translation into conservation practice2015In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 30, no 2, p. 78-87Article in journal (Refereed)
    Abstract [en]

    The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.

  • 35.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Alves, Paulo C.
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Oporto, Portugal.;Fac Ciencias, P-4485661 Oporto, Portugal..
    Bergström, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Colling, Guy
    Musee Natl Hist Nat Luxembourg, Populat Biol, L-2160 Luxembourg, Luxembourg..
    Dalen, Love
    Swedish Museum Nat Hist, Bioinformat & Genet, S-10405 Stockholm, Sweden..
    De Meester, Luc
    KU Leuven Univ Leuven, Aquat Ecol Evolut & Conservat, B-3000 Leuven, Belgium..
    Ekblom, Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Fior, Simone
    Swiss Fed Inst Technol, Integrat Biol, CH-8092 Zurich, Switzerland..
    Hajibabaei, Mehrdad
    Univ Guelph, Integrat Biol, Guelph, ON N1G 2W1, Canada..
    Hoezel, A. Rus
    Univ Durham, Biol & Biomed Sci, Durham DH1 3LE, England..
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jensen, Evelyn L.
    Univ British Columbia Okanagan, Biol, Kelowna, BC V1V 1V7, Canada..
    Kruetzen, Michael
    Univ Zurich, Anthropol Inst & Museum, CH-8057 Zurich, Switzerland..
    Norman, Anita J.
    Swedish Univ Agr Sci, Wildlife Fish & Environm Studies, S-90183 Umea, Sweden..
    Osterling, E. Martin
    Karlstad Univ, Biol, S-65188 Karlstad, Sweden..
    Ouborg, N. Joop
    Radboud Univ Nijmegen, Expt Plant Ecol, NL-6500 GL Nijmegen, Netherlands..
    Piccolo, John
    Primmer, Craig R.
    Univ Turku, Biol, Turku 20014, Finland..
    Reed, Floyd A.
    Univ Hawaii Manoa, Biol, Honolulu, HI 96822 USA..
    Roumet, Marie
    Swiss Fed Inst Technol, Integrat Biol, CH-8092 Zurich, Switzerland..
    Salmona, Jordi
    Inst Gulbenkian Ciencias, Populat & Conservat Genet Grp, P-2780156 Oeiras, Portugal..
    Schwartz, Michael K.
    USDA, Forest Serv, Rocky Mt Res Stn, Missoula, MT 59801 USA..
    Segelbacher, Gernot
    Univ Freiburg, Wildlife Ecol & Management, D-79106 Freiburg, Germany..
    Thaulow, Jens
    Norwegian Inst Water Res, Freshwater Biol, N-0349 Oslo, Norway..
    Valtonen, Mia
    Univ Eastern Finland, Biol, Joensuu 80101, Finland..
    Vergeer, Philippine
    Wageningen Univ, Nat Conservat & Plant Ecol, NL-6708 PB Wageningen, Netherlands..
    Weissensteiner, Matthias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wheat, Christopher W.
    Stockholm Univ, Zool, S-10691 Stockholm, Sweden..
    Vila, Carlese
    Estn Biol Donana, Conservat & Evolutionary Genet Grp, Seville 41092, Spain..
    Zielinski, Piotr
    Jagiellonian Univ, Inst Environm Sci, PL-30387 Krakow, Poland..
    Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application Reply2016In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, no 2, p. 83-84Article in journal (Refereed)
  • 36.
    Shafer, Aaron B A
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B W
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Alves, Paulo C
    Bergström, Linnéa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Colling, Guy
    Dalén, Love
    De Meester, Luc
    Ekblom, Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Fior, Simone
    Hajibabaei, Mehrdad
    Hoezel, A. Rus
    Hoglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jensen, Evelyn L
    Krützen, Michael
    Norman, Anita J.
    Osterling, E. Martin
    Ouborg, N. Joop
    Piccolo, John
    Primmer, Craig R
    Reed, Floyd A
    Roumet, Marie
    Salmona, Jordi
    Schwartz, Michael K
    Segelbacher, Gernot
    Thaulow, Jens
    Valtonen, Mia
    Vergeer, Philippine
    Weissensteiner, Matthias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wheat, Christopher W.
    Vilà, Carlese
    Zielińsk, Piotr
    Reply to Garner et al2016In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, no 2, p. 83-84Article in journal (Refereed)
  • 37. Staubach, Fabian
    et al.
    Teschke, Meike
    Voolstra, Christian R.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Tautz, Diethard
    A test of the neutral model of expression change in natural populations of house mouse subspecies2010In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 64, no 2, p. 549-560Article in journal (Refereed)
    Abstract [en]

    Changes in expression of genes are thought to contribute significantly to evolutionary divergence. To study the relative role of selection and neutrality in shaping expression changes, we analyzed 24 genes in three different tissues of the house mouse (Mus musculus). Samples from two natural populations of the subspecies M. m. domesticus and M. m. musculus were investigated using quantitative PCR assays and sequencing of the upstream region. We have developed an approach to quantify expression polymorphism within such populations and to disentangle technical from biological variation in the data. We found a correlation between expression polymorphism within populations and divergence between populations. Furthermore, we found a correlation between expression polymorphism and sequence polymorphism of the respective genes. These data are most easily interpreted within a framework of a predominantly neutral model of gene expression change, where only a fraction of the changes may have been driven by positive selection. Although most genes investigated were expressed in all three tissues analyzed, significant changes of expression levels occurred predominantly in a single tissue only. This adds to the notion that enhancer-specific effects or transregulatory effects can modulate the evolution of gene expression in a tissue-specific way.

  • 38.
    Stoffel, M. A.
    et al.
    Bielefeld Univ, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany;Liverpool John Moores Univ, Sch Nat Sci & Psychol, Fac Sci, Liverpool L3 3AF, Merseyside, England.
    Humble, E.
    Bielefeld Univ, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany;British Antarctic Survey, Madingley Rd, Cambridge CB3 0ET, England.
    Paijmans, A. J.
    Bielefeld Univ, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.
    Acevedo-Whitehouse, K.
    Autonomous Univ Queretaro, Sch Nat Sci, Unit Basic & Appl Microbiol, Ave Ciencias S-N, Queretaro 76230, Mexico.
    Chilvers, B. L.
    Massey Univ, Inst Vet Anim & Biomed Sci, Wildbase, Private Bag 11222, Palmerston North 4442, New Zealand.
    Dickerson, B.
    NOAA, Natl Marine Mammal Lab, Alaska Fisheries Sci Ctr, Natl Marine Fisheries Serv, Seattle, WA 98115 USA.
    Galimberti, F.
    Elephant Seal Res Grp, Sea Lion Isl FIQQ 1ZZ, Falkland Island.
    Gemmell, N. J.
    Univ Otago, Dept Anat, POB 56, Dunedin 9054, New Zealand.
    Goldsworthy, S. D.
    South Australian Res & Dev Inst, West Beach, SA 5024, Australia.
    Nichols, H. J.
    Bielefeld Univ, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany;Liverpool John Moores Univ, Sch Nat Sci & Psychol, Fac Sci, Liverpool L3 3AF, Merseyside, England;Swansea Univ, Dept Biosci, Swansea SA2 8PP, W Glam, Wales.
    Krueger, O.
    Bielefeld Univ, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.
    Negro, S.
    Univ Paris Saclay, UMR Genet Quantitat & Evolut Le Moulon, INRA, Univ Paris Sud,CNRS,AgroParisTech, F-91190 Gif Sur Yvette, France;Univ Liege, Med Genom BIO3, GIGA R, B-4000 Liege, Belgium.
    Osborne, A.
    Univ Canterbury, Sch Biol Sci, Private Bag 4800, Christchurch 8140, New Zealand.
    Pastor, T.
    EUROPARC Federat, Carretera Esglesia 92, Barcelona 08017, Spain.
    Robertson, B. C.
    Univ Otago, Dept Zool, POB 56, Dunedin 9054, New Zealand.
    Sanvito, S.
    Elephant Seal Res Grp, Sea Lion Isl FIQQ 1ZZ, Falkland Island.
    Schultz, J. K.
    NOAA, Natl Marine Fisheries Serv, 1315 East West Highway, Silver Spring, MD 20910 USA.
    Shafer, A. B. A.
    Trent Univ, Forens Sci & Environm Life Sci, Peterborough, ON K9J 7B8, Canada.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, D-82152 Munich, Germany.
    Hoffman, J. I.
    Bielefeld Univ, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany;British Antarctic Survey, Madingley Rd, Cambridge CB3 0ET, England.
    Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4836Article in journal (Refereed)
    Abstract [en]

    A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we combined genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to evaluate the consequences of commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong signatures of recent population declines. Bottleneck strength is associated with breeding habitat and mating system variation, and together with global abundance explains much of the variation in genetic diversity across species. Overall, bottleneck intensity is unrelated to IUCN status, although the three most heavily bottlenecked species are endangered. Our study reveals an unforeseen interplay between human exploitation, animal biology, demographic declines and genetic diversity.

  • 39. Tao, Yu-Tian
    et al.
    Suo, Fang
    Tusso, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wang, Yan-Kai
    Huang, Song
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Du, Li-Lin
    Intraspecific diversity of fission yeast mitochondrial genomes2019In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 11, no 8, p. 2312-2329Article in journal (Refereed)
    Abstract [en]

    The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.

  • 40.
    Trillmich, Fritz
    et al.
    Univ Bielefeld, Anim Behav, D-33615 Bielefeld, Germany..
    Meise, Kristine
    Univ Bielefeld, Anim Behav, D-33615 Bielefeld, Germany.;Univ Liverpool, Inst Integrat Biol, Dept Ecol Evolut & Behav, Biosci Bldg, Liverpool L69 3BX, Merseyside, England..
    Kalberer, Stephanie
    Univ Bielefeld, Anim Behav, D-33615 Bielefeld, Germany..
    Mueller, Birte
    Univ Munster, Ctr Biol Educ, D-48149 Munster, Germany..
    Piedrahita, Paolo
    Univ Bielefeld, Anim Behav, D-33615 Bielefeld, Germany.;Escuela Super Politecn Litoral, ESPOL, Fac Ciencias Vida, Guayaquil, Ecuador..
    Pörschmann, Ulrich
    Huinay Sci Field Stn, Huinay, Los Lagos, Chile..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Krüger, Oliver
    Univ Bielefeld, Anim Behav, D-33615 Bielefeld, Germany..
    On the Challenge of Interpreting Census Data: Insights from a Study of an Endangered Pinniped2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 5, article id e0154588Article in journal (Refereed)
    Abstract [en]

    Population monitoring is vital for conservation and management. However, simple counts of animals can be misleading and this problem is exacerbated in seals (pinnipeds) where individuals spend much time foraging away from colonies. We analyzed a 13-year-series of census data of Galapagos sea lions (Zalophus wollebaeki) from the colony of Caamano, an islet in the center of the Galapagos archipelago where a large proportion of animals was individually marked. Based on regular resighting efforts during the cold, reproductive (cold-R; August to January) and the warm, non-reproductive (warm-nR; February to May) season, we document changes in numbers for different sex and age classes. During the cold-R season the number of adults increased as the number of newborn pups increased. Numbers were larger in themorning and evening than around mid-day and not significantly influenced by tide levels. More adults frequented the colony during the warm-nR season than the cold-R season. Raw counts suggested a decline in numbers over the 13 years, but Lincoln-Petersen (LP-) estimates (assuming a closed population) did not support that conclusion. Raw counts and LP estimates were not significantly correlated, demonstrating the overwhelming importance of variability in attendance patterns of individuals. The probability of observing a given adult in the colony varied between 16%(mean for cold-R season) and 23%(warm-nR season) and may be much less for independent 2 to 4 year olds. Dependent juveniles (up to the age of about 2 years) are observed much more frequently ashore (35% during the cold-R and 50% during the warm-nR seasons). Simple counts underestimate real population size by a factor of 4-6 and may lead to erroneous conclusions about trends in population size.

  • 41.
    Tusso, Sergio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.
    Nieuwenhuis, Bart P. S.
    Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.
    Sedlazeck, Fritz J.
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX.
    Davey, John W.
    Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom.
    Jeffares, Daniel C.
    Department of Biology, University of York, York, United Kingdom;York Biomedical Research Institute (YBRI), University of York, York, United Kingdom.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.
    Ancestral admixture is the main determinant of global biodiversity in fission yeast2019In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 9, p. 1975-1989Article in journal (Refereed)
    Abstract [en]

    Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred similar to 20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.

  • 42.
    Vijay, Nagarjun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bossu, Christen M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Zool Populat Genet, SE-10691 Stockholm, Sweden..
    Poelstra, Jelmer W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Weissensteiner, Matthias H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kryukov, Alexey P.
    Russian Acad Sci, Inst Biol & Soil Sci, Far East Branch, Lab Evolutionary Zool & Genet, Vladivostok 690022, Russia..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Munich, Div Evolutionary Biol, Grosshaderner St 2, D-82152 Planegg Martinsried, Germany..
    Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 13195Article in journal (Refereed)
    Abstract [en]

    Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.

  • 43.
    Vijay, Nagarjun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Poelstra, Jelmer W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kuenstner, Axel
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 3, p. 620-634Article in journal (Refereed)
    Abstract [en]

    Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism p, alternative splicing), technological processing (sequencing error e, library normalization) and bioinformatic workflow (de novo vs. mapping assembly, reference genome quality) impact transcriptome quality and inference of differential gene expression (DE). We find that transcriptome assembly and gene expression profiling (EdgeR vs. BaySeq software) works well even in the absence of a reference genome and is robust across a broad range of parameters. We advise against library normalization and in most situations advocate mapping assemblies to an annotated genome of a divergent sister clade, which generally outperformed de novo assembly (Trans-Abyss, Trinity, Soapdenovo-Trans). Transcriptome complexity (size, paralogs, alternative splicing isoforms) negatively affected the assembly and DE profiling, whereas the effects of sequencing error and polymorphism were almost negligible. Finally, we highlight the challenge of gene name assignment for de novo assemblies, the importance of mapping strategies and raise awareness of challenges associated with the quality of reference genomes. Overall, our results have significant practical and methodological implications and can provide guidance in the design and analysis of RNA-seq experiments, particularly for organisms where genomic background information is lacking.

  • 44.
    Vijay, Nagarjun
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Michigan, Coll Literature Sci & Arts, Dept Ecol & Evolutionary Biol, Lab Mol & Genom Evolut, Ann Arbor, MI 48109 USA..
    Weissensteiner, Matthias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany..
    Burri, Reto
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Friedrich Schiller Univ Jena, Dept Populat Ecol, Jena, Germany..
    Kawakami, Takeshi
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England..
    Ellegren, Hans
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinsried, Germany..
    Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 16, p. 4284-4295Article in journal (Refereed)
    Abstract [en]

    Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N-e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N-e. Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N-e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (rho), nucleotide diversity (pi) and measures of genetic differentiation between populations (F-ST, PBS, d(xy)) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.

  • 45. von Rönn, J. A. C.
    et al.
    Harrod, C.
    Bensch, S.
    Wolf, Jochen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Transcontinental migratory connectivity predicts parasite prevalence in breeding populations of the European barn swallow2015In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 28, no 3, p. 535-546Article in journal (Refereed)
    Abstract [en]

    Parasites exert a major impact on the eco-evolutionary dynamics of their hosts and the associated biotic environment. Migration constitutes an effective means for long-distance invasions of vector-borne parasites and promotes their rapid spread. Yet, ecological and spatial information on population-specific host-parasite connectivity is essentially lacking. Here, we address this question in a system consisting of a transcontinental migrant species, the European barn swallow (Hirundo rustica) which serves as a vector for avian endoparasites in the genera Plasmodium, Haemoproteus andLeucocytozoon. Using feather stable isotope ratios as geographically informative markers, we first assessed migratory connectivity in the host: Northern European breeding populations predominantly overwintered in dry, savannah-like habitats in Southern Africa, whereas Southern European populations were associated with wetland habitats in Western Central Africa. Wintering areas of swallows breeding in Central Europe indicated a migratory divide with both migratory programmes occurring within the same breeding population. Subsequent genetic screens of parasites in the breeding populations revealed a link between the host's migratory programme and its parasitic repertoire: controlling for effects of local breeding location, prevalence of Africa-transmitted Plasmodium lineages was significantly higher in individuals overwintering in the moist habitats of Western Central Africa, even among sympatrically breeding individuals with different overwintering locations. For the rarer Haemoproteus parasites, prevalence was best explained by breeding location alone, whereas no clear pattern emerged for the least abundant parasite Leucocytozoon. These results have implications for our understanding of spatio-temporal host-parasite dynamics in migratory species and the spread of avian borne diseases.

  • 46.
    von Rönn, Jan A. C.
    et al.
    Max Planck Inst Evolutionary Biol, Dept Evolutionary Genet, August Thienemann Str 2, D-24306 Plon, Germany.;Swiss Ornithol Inst, Seerose 1, CH-6204 Sempach, Switzerland..
    Shafer, Aaron B. A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Max Planck Inst Evolutionary Biol, Dept Evolutionary Genet, August Thienemann Str 2, D-24306 Plon, Germany..
    Disruptive selection without genome-wide evolution across a migratory divide2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 11, p. 2529-2541Article in journal (Refereed)
    Abstract [en]

    Transcontinental migration is a fascinating example of how animals can respond to climatic oscillation. Yet, quantitative data on fitness components are scarce, and the resulting population genetic consequences are poorly understood. Migratory divides, hybrid zones with a transition in migratory behaviour, provide a natural setting to investigate the micro-evolutionary dynamics induced by migration under sympatric conditions. Here, we studied the effects of migratory programme on survival, trait evolution and genome-wide patterns of population differentiation in a migratory divide of European barn swallows. We sampled a total of 824 individuals from both allopatric European populations wintering in central and southern Africa, respectively, along with two mixed populations from within the migratory divide. While most morphological characters varied by latitude consistent with Bergmann's rule, wing length co-varied with distance to wintering grounds. Survival data collected during a 5-year period provided strong evidence that this covariance is repeatedly generated by disruptive selection against intermediate phenotypes. Yet, selection-induced divergence did not translate into genome-wide genetic differentiation as assessed by microsatellites, mtDNA and >20 000 genome-wide SNP markers; nor did we find evidence of local genomic selection between migratory types. Among breeding populations, a single outlier locus mapped to the BUB1 gene with a role in mitotic and meiotic organization. Overall, this study provides evidence for an adaptive response to variation in migration behaviour continuously eroded by gene flow under current conditions of non-assortative mating. It supports the theoretical prediction that population differentiation is difficult to achieve under conditions of gene flow despite measurable disruptive selection.

  • 47.
    Weissensteiner, Matthias H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilian Univ Munich, Fac Biol, Div Evolutionary Biol, D-82152 Planegg Martinsried, Germany..
    Pang, Andy W. C.
    BioNano Genom, San Diego, CA 91121 USA..
    Bunikis, Ignas
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Höijer, Ida
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pettersson, Olga Vinnere
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilian Univ Munich, Fac Biol, Div Evolutionary Biol, D-82152 Planegg Martinsried, Germany..
    Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications2017In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 5, p. 697-708Article in journal (Refereed)
    Abstract [en]

    Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [ OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (rho) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.

  • 48.
    Weissensteiner, Matthias H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Poelstra, Jelmer W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Low-budget ready-to-fly unmanned aerial vehicles: an effective tool for evaluating the nesting status of canopy-breeding bird species2015In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 46, no 4, p. 425-430Article in journal (Refereed)
    Abstract [en]

    Remotely controlled, unmanned aerial vehicles (UAVs) promise to be of high potential for a variety of applications in ecological and behavioural research. Off-the-shelf solutions have recently become available for civil use at steeply decreasing costs. In this study, we explored the utility of an UAV equipped with an on-board camera (14 megapixel photo and 1920 x 1080 pixel video resolution) in assessing the breeding status, offspring number and age of a canopy-breeding bird species, the hooded crow Corvus [corone] cornix. We further quantified performance and potential time savings using the UAV versus inspection with alternative approaches (optical instruments, camera on a telescopic rod, tree climbing). Nesting status, number and approximate age of nestlings could be assessed with good success in all 24 attempts using the UAV. Eighty-five percent of the time required for inspection by climbing could be saved. Disturbance was moderate and lower than caused by climbing or using a camera on a telescopic rod. Additionally, UAV usage avoided tree damage and circumvented health risks associated with tree-climbing.

  • 49.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial2013In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 13, no 4, p. 559-572Article in journal (Refereed)
    Abstract [en]

    Genome-wide analyses and high-throughput screening was long reserved for biomedical applications and genetic model organisms. With the rapid development of massively parallel sequencing nanotechnology (or next-generation sequencing) and simultaneous maturation of bioinformatic tools, this situation has dramatically changed. Genome-wide thinking is forging its way into disciplines like evolutionary biology or molecular ecology that were historically confined to small-scale genetic approaches. Accessibility to genome-scale information is transforming these fields, as it allows us to answer long-standing questions like the genetic basis of local adaptation and speciation or the evolution of gene expression profiles that until recently were out of reach. Many in the eco-evolutionary sciences will be working with large-scale genomic data sets, and a basic understanding of the concepts and underlying methods is necessary to judge the work of others. Here, I briefly introduce next-generation sequencing and then focus on transcriptome shotgun sequencing (RNA-seq). This article gives a broad overview and provides practical guidance for the many steps involved in a typical RNA-seq work flow from sampling, to RNA extraction, library preparation and data analysis. I focus on principles, present useful tools where appropriate and point out where caution is needed or progress to be expected. This tutorial is mostly targeted at beginners, but also contains potentially useful reflections for the more experienced.

  • 50.
    Wolf, Jochen B. W.
    et al.
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemannstr. 2, 24306 Plön, Germany.
    Bayer, Till
    Haubold, Bernhard
    Schilhabel, Markus
    Rosenstiel, Philip
    Tautz, Diethard
    Nucleotide divergence versus gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no Suppl. 1, p. 162-175Article in journal (Refereed)
    Abstract [en]

    Recent advances in sequencing technology promise to provide new strategies for studying population differentiation and speciation phenomena in their earliest phases. We focus here on the black carrion crow (Corvus [corone] corone), which forms a zone of hybridization and overlap with the grey coated hooded crow (Corvus [corone] cornix). However, although these semispecies are taxonomically distinct, previous analyses based on several types of genetic markers did not reveal significant molecular differentiation between them. We here corroborate this result with sequence data obtained from a set of 25 nuclear intronic loci. Thus, the system represents a case of a very early phase of species divergence that requires new molecular approaches for its description. We have therefore generated RNAseq expression profiles using barcoded massively parallel pyrosequencing of brain mRNA from six individuals of the carrion crow and five individuals from a hybrid zone with the hooded crow. We obtained 856 675 reads from two runs, with average read length of 270 nt and coverage of 8.44. Reads were assembled de novo into 19 552 contigs, 70% of which could be assigned to annotated genes in chicken and zebra finch. This resulted in a total of 7637 orthologous genes and a core set of 1301 genes that could be compared across all individuals. We find a clear clustering of expression profiles for the pure carrion crow animals and disperse profiles for the animals from the hybrid zone. These results suggest that gene expression differences may indeed be a sensitive indicator of initial species divergence.

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