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  • 1.
    Dutoit, Ludovic
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Univ Michigan, Dept Ecol & Evolutionary Biol, Lab Mol & Genom Evolut, Ann Arbor, MI USA..
    Mugal, Carina F.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Bossu, Christen M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Stockholm Univ, Dept Zool, S-10691 Stockholm, Sweden.
    Burri, Reto
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Friedrich Schiller Univ, Inst Ecol, Dept Ecol, Dornburger Str 159 07743 Jena, Jena, Germany.
    Wolf, Jochen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Ludwig Maximilians Univ Munchen, Fac Biol 2, Div Evolutionary Biol, Grosshaderner Str 2, D-82152 Martinsried, Germany..
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting2017Ingår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, nr 1849, artikel-id 20162756Artikel i tidskrift (Refereegranskat)
    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.

  • 2.
    Foote, Andrew D.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    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 universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Mancia, Annalaura
    Nielsen, Rasmus
    Qin, Xiang
    Qu, Jiaxin
    Raney, Brian J.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Wolf, Jochen B. W.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Hahn, Matthew W.
    Muzny, Donna M.
    Worley, Kim C.
    Gilbert, M. Thomas P.
    Gibbs, Richard A.
    Convergent evolution of the genomes of marine mammals2015Ingår i: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 47, nr 3, s. 272-275Artikel i tidskrift (Refereegranskat)
    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.

  • 3.
    Foote, Andrew D.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. 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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, 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 ecotypes2016Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, artikel-id 11693Artikel i tidskrift (Refereegranskat)
    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.

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  • 4.
    Knief, Ulrich
    et al.
    Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Munich, Germany.
    Bossu, Christen M.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. 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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Duke Univ, Biol Dept, Durham, NC USA.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Indian Inst Sci Educ & Res, Dept Biol Sci, Bhopal, India.
    Weissensteiner, Matthias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Munich, Germany.
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, 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 zone2019Ingår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, nr 4, s. 570-576Artikel i tidskrift (Refereegranskat)
    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.

  • 5.
    Poelstra, Jelmer W.
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Bossu, Christen M.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Lantz, Henrik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräknings- och systembiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Mueller, I.
    Baglione, V.
    Unneberg, P.
    Wikelski, M.
    Grabherr, Manfred G.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Wolf, Jochen B. W.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The genomic landscape underlying phenotypic integrity in the face of gene flow in crows2014Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, nr 6190, s. 1410-1414Artikel i tidskrift (Refereegranskat)
    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.

  • 6.
    Poelstra, Jelmer W.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Hoeppner, M. P.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Linkopings Univ Victoria Westling, Bioinformat Infrastruct Life Sci, S-58183 Linkoping, Sweden..
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Transcriptomics of colour patterning and coloration shifts in crows2015Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, nr 18, s. 4617-4628Artikel i tidskrift (Refereegranskat)
    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.

  • 7.
    Shafer, Aaron B. A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Alves, Paulo C.
    Bergström, Linnea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Bruford, Michael W.
    Brannstrom, Ioana
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Colling, Guy
    Dalen, Love
    De Meester, Luc
    Ekblom, Robert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Fawcett, Katie D.
    Fior, Simone
    Hajibabaei, Mehrdad
    Hill, Jason A.
    Hoezel, A. Rus
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Vila, Caries
    Weissensteiner, Matthias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Wennerstrom, Lovisa
    Wheat, Christopher W.
    Zielinski, Piotr
    Genomics and the challenging translation into conservation practice2015Ingår i: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 30, nr 2, s. 78-87Artikel i tidskrift (Refereegranskat)
    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.

  • 8.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Speciation genomics: A perspective from vertebrate systems2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Species are vital entities in biology. Species are generally considered to be discrete entities, consisting of a group of (usually interbreeding) individuals that are similar in phenotype and genetic composition, yet differ in significant ways from other species. The study of speciation has focussed on understanding general evolutionary mechanisms involved in the accumulation of differences both at the genetic and phenotypic level. In this thesis, I investigate incipient speciation, an early stage of divergence towards evolutionary independence in closely related natural populations. I make ample use of recent advances in sequencing technology that allow 1) characterizing phenotypic divergence at the level of the transcriptome and 2) delineate patterns of genetic variation at genome-scale from which processes are inferred by using principles of population genetic theory.

    In the first paper, we assembled a draft genome of the hooded crow and investigated population differentiation across a famous European hybrid zone. Comparing sequence differentiation peaks between and within the colour morphs, we could identify regions of the genome that show differentiation only between colour morphs and that could be related to gene expression profiles of the melanogenesis pathway coding for colour differences.

    The second paper expands on the first paper in that it includes crow population samples from across the entire Palaearctic distribution spanning two additional zones of contact between colour morphs. The results suggest that regions associated with selection against gene flow between colour morphs were largely idiosyncratic to each contact zone and emerged against a background of conserved 'islands of differentiation' due to shared linked selection.

    The third paper focusses on five killer whale ecotypes with distinct feeding and habitat specific adaptations. Differing levels of sequence differentiation between these ecotypes places them along a speciation continuum and provides a unique temporal cross-section of the speciation process. Using genome scans we identified regions of the genome that show ecotype specific differentiation patterns which might contain candidate genes involved in adaptation.

    In the fourth and final paper, I assumed a comparative genomic perspective to the problem of heterogeneous genomic differentiation during population divergence. The relatively high correlations in the diversity landscapes as well as differentiation patterns between crow, flycatcher and Darwin's Finch populations is best explained by conservation in broad-scale recombination rate and/or  association with telomeres and centromeres conducive to shared, linked selection.

    Delarbeten
    1. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
    Öppna denna publikation i ny flik eller fönster >>The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
    Visa övriga...
    2014 (Engelska)Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, nr 6190, s. 1410-1414Artikel i tidskrift (Refereegranskat) Published
    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.

    Nationell ämneskategori
    Evolutionsbiologi Genetik
    Identifikatorer
    urn:nbn:se:uu:diva-228535 (URN)10.1126/science.1253226 (DOI)000337531700043 ()
    Tillgänglig från: 2014-07-17 Skapad: 2014-07-16 Senast uppdaterad: 2017-12-05Bibliografiskt granskad
    2. Idiosyncratic patterns and processes of genomic differentiation in replicate contact zones in crows
    Öppna denna publikation i ny flik eller fönster >>Idiosyncratic patterns and processes of genomic differentiation in replicate contact zones in crows
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    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nyckelord
    speciation, hybrid zone, linked selection, crow, diversity
    Nationell ämneskategori
    Naturvetenskap
    Forskningsämne
    Biologi med inriktning mot evolutionär genetik
    Identifikatorer
    urn:nbn:se:uu:diva-266263 (URN)
    Tillgänglig från: 2015-11-10 Skapad: 2015-11-05 Senast uppdaterad: 2016-01-13
    3. Genome-culture coevolution promotes rapid divergence in the killer whale
    Öppna denna publikation i ny flik eller fönster >>Genome-culture coevolution promotes rapid divergence in the killer whale
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    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Naturvetenskap
    Forskningsämne
    Biologi med inriktning mot evolutionär genetik
    Identifikatorer
    urn:nbn:se:uu:diva-265341 (URN)
    Tillgänglig från: 2015-11-05 Skapad: 2015-10-27 Senast uppdaterad: 2016-01-13
    4. Genomic signatures of species diversification – a comparative perspective
    Öppna denna publikation i ny flik eller fönster >>Genomic signatures of species diversification – a comparative perspective
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-267095 (URN)
    Tillgänglig från: 2015-11-17 Skapad: 2015-11-17 Senast uppdaterad: 2016-01-13
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  • 9.
    Vijay, Nagarjun
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Bossu, Christen M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Zool Populat Genet, SE-10691 Stockholm, Sweden..
    Poelstra, Jelmer W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Weissensteiner, Matthias H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Suh, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, 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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, 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 complex2016Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, artikel-id 13195Artikel i tidskrift (Refereegranskat)
    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.

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  • 10.
    Vijay, Nagarjun
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Poelstra, Jelmer W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Kuenstner, Axel
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments2013Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, nr 3, s. 620-634Artikel i tidskrift (Refereegranskat)
    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.

  • 11.
    Zamani, Neda
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Russell, Pamela
    Lantz, Henrik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Hoeppner, Marc
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Meadows, Jennifer
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Mauceli, Evan
    di Palma, Federica
    Lindblad-Toh, Kerstin
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Jern, Patric
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Grabherr, Manfred
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Unsupervised genome-wide recognition of local relationship patterns2013Ingår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 14, s. 347-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    BACKGROUND

    Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion.

    RESULTS

    We developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems.

    CONCLUSIONS

    Saguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro's utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.

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