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  • 1.
    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.

  • 2.
    Peona, Valentina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Weissensteiner, Matthias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig-Maximilian University of Munich.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    How complete are "complete" genome assemblies?: An avian perspective2018In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, no 6, p. 1188-1195Article in journal (Refereed)
    Abstract [en]

    The genomics revolution has led to the sequencing of a large variety of non-model organisms often referred to as 'whole' or 'complete' genome assemblies. But how complete are these, really? Here we use birds as an example for non-model vertebrates and find that, although suitable in principle for genomic studies, the current standard of short-read assemblies misses a significant proportion of the expected genome size (7 to 42%; mean 20 ± 9%). In particular, regions with strongly deviating nucleotide composition (e.g., guanine-cytosine-[GC]-rich) and regions highly enriched in repetitive DNA (e.g., transposable elements and satellite DNA) are usually underrepresented in assemblies. However, long-read sequencing technologies successfully characterize many of these underrepresented GC-rich or repeat-rich regions in several bird genomes. For instance, only ~2% of the expected total base pairs are missing in the last chicken reference (galGal5). These assemblies still contain thousands of gaps (i.e., fragmented sequences) because some chromosomal structures (e.g., centromeres) likely contain arrays of repetitive DNA that are too long to bridge with currently available technologies. We discuss how to minimize the number of assembly gaps by combining the latest available technologies with complementary strengths. Finally, we emphasize the importance of knowing the location, size, and potential content of assembly gaps when making population genetic inferences about adjacent genomic regions.

  • 3.
    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.

  • 4.
    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)
  • 5.
    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)
  • 6.
    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.

  • 7.
    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.

  • 8.
    Weissensteiner, Matthias H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Evolutionary genomics in Corvids: – From single nucleotides to structural variants2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Heritable genetic variation is the raw material of evolution and can occur in many different forms, from altering single nucleotides to rearranging stretches of millions at once. DNA mutations that result in phenotypic differences are the basis upon which natural selection can act, leading to a shift of the frequency of those mutations.

    In this thesis I aim to comprehensively characterize and quantify genetic variation in a natural system, the songbird genus Corvus.

    First, we expand on previous work from a hybrid zone of different populations of Eurasian crows. All black carrion crows and black-and-grey hooded crows meet in a narrow hybrid zone in central Europe, and also in central and Southeast Asia. Comparing population genetic data acquired from these three hybrid zones yielded no single genetic region as a candidate responsible for phenotypic divergence, yet a parallelism in sets of genes and gene networks was evident.

    Second, we capitalize on varying evolutionary timescales to investigate the driver of the heterogeneous genetic differentiation landscape observed in multiple avian species. Genetic diversity, and thus differentiation, seems to be correlated both between populations within single species and between species which diverged 50 million years ago. This pattern is best explained by conserved broad-scale recombination rate variation, which is in turn likely associated with chromosomal features such as centromeres and telomeres.

    Third, we introduce a de-novo assembly of the hooded crow based on long-read sequencing and optical mapping. The use of this technology allowed a glimpse into previously hidden regions of the genome, and uncovered large-scale tandem repeat arrays consisting of a 14-kbp satellite repeat or its 1.2-kpb subunit. Furthermore, these tandem repeat arrays are associated with regions of reduced recombination rate.

    Lastly, we extend the population genetic analysis to structural genomic variation, such as insertions and deletions. A large-scale population re-sequencing data set based on short-read and long-read technologies, spread across the entire genus is the foundation of a fine-scale genome-wide map of structural variation. A differentiation outlier approach between all-black carrion and black-and-grey hooded crows identified a 2.25-kilobase LTR retrotransposon inserted 20-kb upstream of the NDP gene. The element, which is fixed in the hooded crow population, is associated with decreased expression of NDP and may be responsible for differences in plumage color.

    List of papers
    1. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
    Open this publication in new window or tab >>Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
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    2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 13195Article in journal (Refereed) Published
    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.

    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-308915 (URN)10.1038/ncomms13195 (DOI)000386500600001 ()27796282 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536
    Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2019-01-07Bibliographically approved
    2. Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa
    Open this publication in new window or tab >>Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa
    Show others...
    2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 16, p. 4284-4295Article in journal (Refereed) Published
    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.

    Place, publisher, year, edition, pages
    WILEY, 2017
    Keywords
    background selection, genetic diversity, genetic draft, genetic hitchhiking, linked selection, recombination rate, speciation genetics
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-333716 (URN)10.1111/mec.14195 (DOI)000407255100013 ()28570015 (PubMedID)
    Funder
    Swedish Research Council, 621-2010-5553, 2014-6325, 2013-08721EU, European Research Council, ERCStG-336536Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)
    Available from: 2017-11-16 Created: 2017-11-16 Last updated: 2019-01-07Bibliographically approved
    3. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
    Open this publication in new window or tab >>Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
    Show others...
    2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 5, p. 697-708Article in journal (Refereed) Published
    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.

    Place, publisher, year, edition, pages
    COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2017
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-323040 (URN)10.1101/gr.215095.116 (DOI)000400392400005 ()28360231 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)Swedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536
    Available from: 2017-06-01 Created: 2017-06-01 Last updated: 2019-01-07Bibliographically approved
    4. Fine-scale analysis of Structural Genomic Variation in Natural Populations
    Open this publication in new window or tab >>Fine-scale analysis of Structural Genomic Variation in Natural Populations
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    (English)Manuscript (preprint) (Other (popular science, discussion, etc.))
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-369880 (URN)
    Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07
  • 9.
    Weissensteiner, Matthias H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Division of Evolutionary Biology Faculty of Biology Ludwig-Maximilians-Universität München Grosshaderner Strasse 2 82152 Planegg-Martinsried GERMANY.
    Bunikis, Ignas
    Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.
    Knief, Ulrich
    2Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
    Peona, Valentina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Pophaly, Saurabh D.
    2Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sedlazeck, Fritz J.
    5Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
    Warmuth, Vera
    2Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
    Wolf, Jochen B.W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. 2Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
    Fine-scale analysis of Structural Genomic Variation in Natural PopulationsManuscript (preprint) (Other (popular science, discussion, etc.))
  • 10.
    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.

  • 11.
    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.

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