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  • 1.
    Boman, Jesper
    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.
    Frankl-Vilches, Carolina
    Max Planck Inst Ornithol, Dept Behav Neurobiol, D-82319 Seewiesen, Germany.
    dos Santos, Michelly da Silva
    Inst Evandro Chagas, SAMAM, Lab Cultura Tecidos & Citogenet, Ananindeua, Para, Brazil;Univ Fed Para, Fac Ciencias Nat ICEN, BR-66075110 Belem, Para, Brazil.
    de Oliveira, Edivaldo H. C.
    Inst Evandro Chagas, SAMAM, Lab Cultura Tecidos & Citogenet, Ananindeua, Para, Brazil;Univ Fed Para, Fac Ciencias Nat ICEN, BR-66075110 Belem, Para, Brazil.
    Gahr, Manfred
    Max Planck Inst Ornithol, Dept Behav Neurobiol, D-82319 Seewiesen, Germany.
    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.
    The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 4, article id 301Article in journal (Refereed)
    Abstract [en]

    Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.

  • 2.
    Burri, Reto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nater, Alexander
    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.
    Mugal, Carina F.
    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 Cell and Molecular Biology, Molecular Evolution.
    Smeds, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dutoit, Ludovic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bures, Stanislav
    Palacky Univ, Dept Zool, Lab Ornithol, Olomouc 77146, Czech Republic..
    Garamszegi, Laszlo Z.
    CSIC, Dept Evolutionary Ecol, Estn Biol Donana, Seville 41092, Spain..
    Hogner, Silje
    Univ Oslo, Ctr Ecol & Evolutionary Synth, Dept Biosci, N-0316 Oslo, Norway.;Univ Oslo, Nat Hist Museum, N-0318 Oslo, Norway..
    Moreno, Juan
    CSIC, Museo Nacl Ciencias Nat, E-28006 Madrid, Spain..
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ruzic, Milan
    Bird Protect & Study Soc Serbia, Novi Sad 21000, Serbia..
    Saether, Stein-Are
    Univ Oslo, Ctr Ecol & Evolutionary Synth, Dept Biosci, N-0316 Oslo, Norway.;Norwegian Inst Nat Res NINA, N-7034 Trondheim, Norway..
    Saetre, Glenn-Peter
    Univ Oslo, Ctr Ecol & Evolutionary Synth, Dept Biosci, N-0316 Oslo, Norway..
    Toeroek, Janos
    Eotvos Lorand Univ, Dept Systemat Zool & Ecol, Behav Ecol Grp, H-1117 Budapest, Hungary..
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers2015In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 25, no 11, p. 1656-1665Article in journal (Refereed)
    Abstract [en]

    Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation ("differentiation islands") widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (d(XY) relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.

  • 3.
    Craig, Rory J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Edinburgh, Sch Biol Sci, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wang, Mi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 2, p. 476-492Article in journal (Refereed)
    Abstract [en]

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

  • 4. Green, Richard E.
    et al.
    Braun, Edward L.
    Armstrong, Joel
    Earl, Dent
    Nguyen, Ngan
    Hickey, Glenn
    Vandewege, Michael W.
    St John, John A.
    Capella-Gutierrez, Salvador
    Castoe, Todd A.
    Kern, Colin
    Fujita, Matthew K.
    Opazo, Juan C.
    Jurka, Jerzy
    Kojima, Kenji K.
    Caballero, Juan
    Hubley, Robert M.
    Smit, Arian F.
    Platt, Roy N.
    Lavoie, Christine A.
    Ramakodi, Meganathan P.
    Finger, John W.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Isberg, Sally R.
    Miles, Lee
    Chong, Amanda Y.
    Jaratlerdsiri, Weerachai
    Gongora, Jaime
    Moran, Christopher
    Iriarte, Andres
    McCormack, John
    Burgess, Shane C.
    Edwards, Scott V.
    Lyons, Eric
    Williams, Christina
    Breen, Matthew
    Howard, Jason T.
    Gresham, Cathy R.
    Peterson, Daniel G.
    Schmitz, Juergen
    Pollock, David D.
    Haussler, David
    Triplett, Eric W.
    Zhang, Guojie
    Irie, Naoki
    Jarvis, Erich D.
    Brochu, Christopher A.
    Schmidt, Carl J.
    McCarthy, Fiona M.
    Faircloth, Brant C.
    Hoffmann, Federico G.
    Glenn, Travis C.
    Gabaldon, Toni
    Paten, Benedict
    Ray, David A.
    Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 346, no 6215, p. 1335-+Article in journal (Refereed)
    Abstract [en]

    To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

  • 5.
    Holt, Carson
    et al.
    Dept Human Genet, Vienna, Austria;USTAR Ctr Genet Discovery, Vienna, Austria.
    Campbell, Michael
    Dept Human Genet, Vienna, Austria;Cold Spring Harbor Lab, Div Plant Biol, POB 100, Cold Spring Harbor, NY 11724 USA.
    Keays, David A.
    Res Inst Mol Pathol, Vienna, Austria.
    Edelman, Nathaniel
    Res Inst Mol Pathol, Vienna, Austria;Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA.
    Kapusta, Aurelie
    Dept Human Genet, Vienna, Austria;USTAR Ctr Genet Discovery, Vienna, Austria.
    Maclary, Emily
    Univ Utah, Dept Biol, 257 S 1400 E, Salt Lake City, UT 84108 USA.
    Domyan, Eric T.
    Univ Utah, Dept Biol, 257 S 1400 E, Salt Lake City, UT 84108 USA;Utah Valley Univ, Dept Biol, Orem, UT USA.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Warren, Wesley C.
    Washington Univ, Genome Inst, St Louis, MO USA.
    Yandell, Mark
    Dept Human Genet, Vienna, Austria;USTAR Ctr Genet Discovery, Vienna, Austria.
    Gilbert, M. Thomas P.
    Univ Copenhagen, Nat Hist Museum Denmark, Copenhagen, Denmark;Norwegian Univ Sci & Technol, Univ Museum, Trondheim, Norway.
    Shapiro, Michael D.
    Univ Utah, Dept Biol, 257 S 1400 E, Salt Lake City, UT 84108 USA.
    Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)2018In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 5, p. 1391-1398Article in journal (Refereed)
    Abstract [en]

    The domestic rock pigeon (Columba livia) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general.

  • 6.
    Jarvis, Erich D.
    et al.
    Duke Univ, Med Ctr, Howard Hughes Med Inst, Dept Neurobiol, Durham, NC 27710 USA.;Duke Univ, Med Ctr, Durham, NC 27710 USA..
    Mirarab, Siavash
    Univ Texas Austin, Dept Comp Sci, Austin, TX 78712 USA..
    Aberer, Andre J.
    Heidelberg Inst Theoret Studies, Sci Comp Grp, Heidelberg, Germany..
    Li, Bo
    BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.;Xi An Jiao Tong Univ, Coll Med & Forens, Xian 710061, Peoples R China.;Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Houde, Peter
    New Mexico State Univ, Dept Biol, Las Cruces, NM 88003 USA..
    Li, Cai
    BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.;Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Ho, Simon Y. W.
    Univ Sydney, Sch Biol Sci, Sydney, NSW 2006, Australia..
    Faircloth, Brant C.
    Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA.;Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA..
    Nabholz, Benoit
    Univ Montpellier 2, CNRS, UMR 5554, Inst Sci Evolut Montpellier, Montpellier, France..
    Howard, Jason T.
    Duke Univ, Med Ctr, Howard Hughes Med Inst, Dept Neurobiol, Durham, NC 27710 USA.;Duke Univ, Med Ctr, Durham, NC 27710 USA..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Weber, Claudia C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    da Fonseca, Rute R.
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Alfaro-Nunez, Alonzo
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Narula, Nitish
    New Mexico State Univ, Dept Biol, Las Cruces, NM 88003 USA.;Okinawa Inst Sci & Technol Onna Son, Biodivers & Biocomplex Unit, Okinawa 9040495, Japan..
    Liu, Liang
    Univ Georgia, Dept Stat, Athens, GA 30602 USA.;Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA..
    Burt, Dave
    Univ Edinburgh, Roslin Inst, Dept Genom & Genet, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Roslin EH25 9RG, Midlothian, Scotland..
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Edwards, Scott V.
    Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA.;Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA..
    Stamatakis, Alexandros
    Heidelberg Inst Theoret Studies, Sci Comp Grp, Heidelberg, Germany.;Karlsruhe Inst Technol, Dept Informat, Inst Theoret Informat, D-76131 Karlsruhe, Germany..
    Mindell, David P.
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94158 USA..
    Cracraft, Joel
    Amer Museum Nat Hist, Dept Ornithol, New York, NY 10024 USA..
    Braun, Edward L.
    Univ Florida, Dept Biol, Gainesville, FL 32611 USA.;Univ Florida, Genet Inst, Gainesville, FL 32611 USA..
    Warnow, Tandy
    Univ Texas Austin, Dept Comp Sci, Austin, TX 78712 USA..
    Jun, Wang
    BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.;Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark.;King Abdulaziz Univ, Princess Al Jawhara Ctr Excellence Res Hereditary, Jeddah 21589, Saudi Arabia.;Macau Univ Sci & Technol, Taipa 999078, Peoples R China.;Univ Hong Kong, Dept Med, Hong Kong, Hong Kong, Peoples R China..
    Gilbert, M. Thomas Pius
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Curtin Univ, Dept Environm & Agr, Trace & Environm DNA Lab, Perth, WA 6102, Australia..
    Zhang, Guojie
    BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.;Univ Copenhagen, Dept Biol, Ctr Social Evolut, DK-2100 Copenhagen, Denmark..
    Phylogenomic analyses data of the avian phylogenomics project2015In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 4, article id 4Article in journal (Refereed)
    Abstract [en]

    Background: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. Findings: Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. Conclusions: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

  • 7. Jarvis, Erich D.
    et al.
    Mirarab, Siavash
    Aberer, Andre J.
    Li, Bo
    Houde, Peter
    Li, Cai
    Ho, Simon Y. W.
    Faircloth, Brant C.
    Nabholz, Benoit
    Howard, Jason T.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Weber, Claudia C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    da Fonseca, Rute R.
    Li, Jianwen
    Zhang, Fang
    Li, Hui
    Zhou, Long
    Narula, Nitish
    Liu, Liang
    Ganapathy, Ganesh
    Boussau, Bastien
    Bayzid, Md. Shamsuzzoha
    Zavidovych, Volodymyr
    Subramanian, Sankar
    Gabaldon, Toni
    Capella-Gutierrez, Salvador
    Huerta-Cepas, Jaime
    Rekepalli, Bhanu
    Munch, Kasper
    Schierup, Mikkel
    Lindow, Bent
    Warren, Wesley C.
    Ray, David
    Green, Richard E.
    Bruford, Michael W.
    Zhan, Xiangjiang
    Dixon, Andrew
    Li, Shengbin
    Li, Ning
    Huang, Yinhua
    Derryberry, Elizabeth P.
    Bertelsen, Mads Frost
    Sheldon, Frederick H.
    Brumfield, Robb T.
    Mello, Claudio V.
    Lovell, Peter V.
    Wirthlin, Morgan
    Cruz Schneider, Maria Paula
    Prosdocimi, Francisco
    Samaniego, Jose Alfredo
    Vargas Velazquez, Amhed Missael
    Alfaro-Nunez, Alonzo
    Campos, Paula F.
    Petersen, Bent
    Sicheritz-Ponten, Thomas
    Pas, An
    Bailey, Tom
    Scofield, Paul
    Bunce, Michael
    Lambert, David M.
    Zhou, Qi
    Perelman, Polina
    Driskell, Amy C.
    Shapiro, Beth
    Xiong, Zijun
    Zeng, Yongli
    Liu, Shiping
    Li, Zhenyu
    Liu, Binghang
    Wu, Kui
    Xiao, Jin
    Yinqi, Xiong
    Zheng, Qiuemei
    Zhang, Yong
    Yang, Huanming
    Wang, Jian
    Smeds, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rheindt, Frank E.
    Braun, Michael
    Fjeldsa, Jon
    Orlando, Ludovic
    Barker, F. Keith
    Jonsson, Knud Andreas
    Johnson, Warren
    Koepfli, Klaus-Peter
    O'Brien, Stephen
    Haussler, David
    Ryder, Oliver A.
    Rahbek, Carsten
    Willerslev, Eske
    Graves, Gary R.
    Glenn, Travis C.
    McCormack, John
    Burt, Dave
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Alstrom, Per
    Edwards, Scott V.
    Stamatakis, Alexandros
    Mindell, David P.
    Cracraft, Joel
    Braun, Edward L.
    Warnow, Tandy
    Jun, Wang
    Gilbert, M. Thomas P.
    Zhang, Guojie
    Whole-genome analyses resolve early branches in the tree of life of modern birds2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 346, no 6215, p. 1320-1331Article in journal (Refereed)
    Abstract [en]

    To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

  • 8.
    Kapusta, Aurelie
    et al.
    Univ Utah, Sch Med, Dept Human Genet, Salt Lake City, UT 84132 USA..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Evolution of bird genomes-a transposon's-eye view2017In: Annals of the New York Academy of Sciences, ISSN 0077-8923, E-ISSN 1749-6632, Vol. 1389, no 1, p. 164-185Article, review/survey (Refereed)
    Abstract [en]

    Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE "arms races" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.

  • 9.
    Kapusta, Aurelie
    et al.
    Univ Utah, Sch Med, Dept Human Genet, Salt Lake City, UT 84112 USA..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Feschotte, Cedric
    Univ Utah, Sch Med, Dept Human Genet, Salt Lake City, UT 84112 USA..
    Dynamics of genome size evolution in birds and mammals2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 8, p. E1460-E1469Article in journal (Refereed)
    Abstract [en]

    Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (> 10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.

  • 10.
    Kawakami, Takeshi
    et al.
    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..
    Mugal, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nater, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland..
    Burri, Reto
    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..
    Smeds, Linnea
    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.
    Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 16, p. 4158-4172Article in journal (Refereed)
    Abstract [en]

    Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.

  • 11. Kutter, C
    et al.
    Jern, Patric
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Suh, Alexander
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bridging gaps in transposable element research with single-molecule and single-cell technologies2018In: Mobile DNA, ISSN 1759-8753, E-ISSN 1759-8753, Vol. 9, article id 34Article in journal (Refereed)
    Abstract [en]

    More than half of the genomic landscape in humans and many other organisms is composed of repetitive DNA, which mostly derives from transposable elements (TEs) and viruses. Recent technological advances permit improved assessment of the repetitive content across genomes and newly developed molecular assays have revealed important roles of TEs and viruses in host genome evolution and organization. To update on our current understanding of TE biology and to promote new interdisciplinary strategies for the TE research community, leading experts gathered for the 2nd Uppsala Transposon Symposium on October 4&#226;€“5, 2018 in Uppsala, Sweden. Using cutting-edge single-molecule and single-cell approaches, research on TEs and other repeats has entered a new era in biological and biomedical research.

  • 12.
    Lauber, Chris
    et al.
    Tech Univ Dresden, Inst Med Informat & Biometry, D-01307 Dresden, Germany..
    Seitz, Stefan
    Heidelberg Univ, Dept Infect Dis, Mol Virol, D-69120 Heidelberg, Germany..
    Mattei, Simone
    European Mol Biol Lab, Struct & Computat Biol Unit, D-69117 Heidelberg, Germany..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Beck, Juergen
    Univ Hosp Freiburg, Dept Internal Med Mol Biol 2, D-79106 Freiburg, Germany..
    Herstein, Jennifer
    Univ Southern Calif, Keck Sch Med, Dept Psychiat & Behav Sci, Los Angeles, CA 90033 USA..
    Boerold, Jacob
    Heidelberg Univ, Dept Infect Dis, Mol Virol, D-69120 Heidelberg, Germany..
    Salzburger, Walter
    Univ Basel, Inst Zool, CH-4051 Basel, Switzerland..
    Kaderali, Lars
    Tech Univ Dresden, Inst Med Informat & Biometry, D-01307 Dresden, Germany.;Univ Med Greifswald, Inst Bioinformat, D-17487 Greifswald, Germany..
    Briggs, John A. G.
    European Mol Biol Lab, Struct & Computat Biol Unit, D-69117 Heidelberg, Germany..
    Bartenschlager, Ralf
    Heidelberg Univ, Dept Infect Dis, Mol Virol, D-69120 Heidelberg, Germany.;German Canc Res Ctr, Div Virus Associated Carcinogenesis, D-69120 Heidelberg, Germany..
    Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses2017In: Cell Host and Microbe, ISSN 1931-3128, E-ISSN 1934-6069, Vol. 22, no 3, p. 387-399,e1-e6Article in journal (Refereed)
    Abstract [en]

    Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome organization with extensive gene overlap. Remarkably, the similar to 1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of HBVs including genome replication via proteinprimed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction indicates that these two virus families separated more than 400 million years ago before the rise of tetrapods. We show that HBVs are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo, leading to a major transition in viral lifestyle, followed by co-evolution with their hosts over geologic eras.

  • 13.
    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.

  • 14. Platt, Roy N., II
    et al.
    Zhang, Yuhua
    Witherspoon, David J.
    Xing, Jinchuan
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Keith, Megan S.
    Jorde, Lynn B.
    Stevens, Richard D.
    Ray, David A.
    Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis2015In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 7, no 6, p. 1664-1675Article in journal (Refereed)
    Abstract [en]

    Identification of retrotransposon insertions in nonmodel taxa can be technically challenging and costly. This has inhibited progress in understanding retrotransposon insertion dynamics outside of a few well-studied species. To address this problem, we have extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis. We identified between 120,000 and 143,000 SINE insertions in six taxa lacking a draft genome by comparing to the M. lucifugus reference genome. On average, eachVes insertion was sequenced to 129.6 x coverage. When mapped back to the M. lucifugus reference genome, all insertions were confidently assigned within a 10-bp window. Polymorphic Ves insertions were identified in each taxon based on their mapped locations. Using cross-species comparisons and the identified insertion positions, a presence-absence matrix was created for approximately 796,000 insertions. Dollo parsimony analysis of more than 85,000 phylogenetically informative insertions recovered strongly supported, monophyletic clades that correspond with the biogeography of each taxa. This phylogeny is similar to previously published mitochondrial phylogenies, with the exception of the placement of M. vivesi. These results support the utility of our variation on ME-Scan to identify polymorphic retrotransposon insertions in taxa without a reference genome and for large-scale retrotransposon-based phylogenetics.

  • 15.
    Prost, Stefan
    et al.
    Swedish Museum Nat Hist, Dept Biodivers & Genet, Frescativaegen 40, S-10401 Stockholm, Sweden;Univ Calif Berkeley, Dept Integrat Biol, 3040 Valley Life Sci Bldg, Berkeley, CA 94720 USA.
    Armstrong, Ellie E.
    Stanford Univ, Dept Biol, 371 Serra Mall, Stanford, CA 94305 USA.
    Nylander, Johan
    Swedish Museum Nat Hist, Dept Biodivers & Genet, Frescativaegen 40, S-10401 Stockholm, Sweden.
    Thomas, Gregg W. C.
    Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA;Indiana Univ, Sch Informat Comp & Engn, 1001 E Third St, Bloomington, IN 47405 USA.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Petersen, Bent
    Univ Copenhagen, Nat Hist Museum Denmark, Oster Voldgade 5-7, DK-1353 Copenhagen, Denmark;Asian Inst Med Sci & Technol, Fac Appl Sci, Ctr Excellence Omics Driven Computat Biodiscovery, Jalan Bedong Semeling, Bedong 08100, Kedah, Malaysia.
    Dalen, Love
    Swedish Museum Nat Hist, Dept Biodivers & Genet, Frescativaegen 40, S-10401 Stockholm, Sweden.
    Benz, Brett W.
    Amer Museum Nat Hist, Dept Ornithol, Cent Pk West, New York, NY 10024 USA.
    Blom, Mozes P. K.
    Swedish Museum Nat Hist, Dept Biodivers & Genet, Frescativaegen 40, S-10401 Stockholm, Sweden.
    Palkopoulou, Eleftheria
    Swedish Museum Nat Hist, Dept Biodivers & Genet, Frescativaegen 40, S-10401 Stockholm, Sweden.
    Ericson, Per G. P.
    Swedish Museum Nat Hist, Dept Biodivers & Genet, Frescativaegen 40, S-10401 Stockholm, Sweden.
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Biodivers & Genet, Frescativaegen 40, S-10401 Stockholm, Sweden.
    Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise2019In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 8, no 5, article id giz003Article in journal (Refereed)
    Abstract [en]

    The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for "startle response" and "olfactory receptor activity" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.

  • 16.
    Schweizer, Manuel
    et al.
    Nat Hist Museum Bern, Bern, Switzerland.
    Warmuth, Vera
    Ludwig Maximilians Univ Munchen, Dept Biol 2, Evolutionary Biol, Martinsried, Germany.
    Kakhki, Niloofar Alaei
    Ferdowsi Univ Mashhad, Dept Biol, Fac Sci, Mashhad, Iran.
    Aliabadian, Mansour
    Ferdowsi Univ Mashhad, Dept Biol, Fac Sci, haMashd, Iran.
    Foerschler, Marc
    Black Forest Natl Pk, Dept Ecosyst Monitoring Res & Conservat, Freudenstadt, Germany.
    Shirihai, Hadoram
    Zürich, Switzerland.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, Jena, Germany.
    Parallel plumage colour evolution and introgressive hybridization in wheatears2019In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 32, no 1, p. 100-110Article in journal (Refereed)
    Abstract [en]

    Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa-pied wheatear (O. pleschanka), Cyprus wheatear (Oenanthe cypriaca), and western and eastern subspecies of black-eared wheatear (O. h. hispanica and O. h. melanoleuca). Phenotypically, black back and neck sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20,000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of colour phenotypes and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage colour evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.

  • 17.
    Smeds, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Warmuth, Vera
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bolivar, Paulina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Uebbing, Severin
    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.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nater, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bures, Stanislav
    Garamszegi, Laszlo Z.
    Hogner, Silje
    Moreno, Juan
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ruzic, Milan
    Saether, Stein-Are
    Saetre, Glenn-Peter
    Torok, Janos
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Evolutionary analysis of the female-specific avian W chromosome2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7330Article in journal (Refereed)
    Abstract [en]

    The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear-cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution.

  • 18.
    Sotero-Caio, Cibele G.
    et al.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Platt, Roy N., II
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ray, David A.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Evolution and Diversity of Transposable Elements in Vertebrate Genomes2017In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 1, p. 161-177Article in journal (Refereed)
    Abstract [en]

    Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genomeevolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.

  • 19.
    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.
    Genome Size Evolution: Small Transposons with Large Consequences2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 7, p. R241-R243Article in journal (Refereed)
    Abstract [en]

    Transposable elements (TEs) heavily influence genome size variation between organisms. A new study on larvacean tunicates now shows that even non-autonomous TEs - small TEs that parasitize the enzymatic machinery of large, autonomous TEs - can have a large impact on genome size.

  • 20.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves2016In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 45, p. 50-62Article, review/survey (Refereed)
    Abstract [en]

    Birds have arguably been the most intensely studied animal group for their phylogenetic relationships. However, the recent advent of genome-scale phylogenomics has made the forest of bird phylogenies even more complex and confusing. Here, in this perspective piece, I show that most parts of the avian Tree of Life are now firmly established as reproducible phylogenetic hypotheses. This is to the exception of the deepest relationships among Neoaves. Using phylogenetic networks and simulations, I argue that the very onset of the super-rapid neoavian radiation is irresolvable because of eight near-simultaneous speciation events. Such a hard polytomy of nine taxa translates into 2 027 025 possible rooted bifurcating trees. Accordingly, recent genome-scale phylogenies show extremely complex conflicts in this (and only this) part of the avian Tree of Life. I predict that the upcoming years of avian phylogenomics will witness many more, highly conflicting tree topologies regarding the early neoavian polytomy. I further caution against bootstrapping in the era of genomics and suggest to instead use reproducibility (e.g. independent methods or data types) as support for phylogenetic hypotheses. The early neoavian polytomy coincides with the Cretaceous-Paleogene (K-Pg) mass extinction and is, to my knowledge, the first empirical example of a hard polytomy.

  • 21.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The Specific Requirements for CR1 Retrotransposition Explain the Scarcity of Retrogenes in Birds2015In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 81, no 1-2, p. 18-20Article in journal (Refereed)
    Abstract [en]

    Chicken repeat 1 (CR1) retroposons are the most abundant superfamily of transposable elements in the genomes of birds, crocodilians, and turtles. However, CR1 mobilization remains poorly understood. In this article, I document that the diverse CR1 lineages of land vertebrates share a highly conserved hairpin structure and an octamer microsatellite motif at their very 3' ends. Together with the presence of these same motifs in the tails of CR1-mobilized short interspersed elements, this suggests that the minimum requirement for CR1 transcript recognition and retrotransposition is a complex > 50-nt structure. Such a highly specific recognition sequence readily explains why CR1-dominated genomes generally contain very few retrogenes. Conversely, the mammalian richness in retrogenes results from CR1 extinction in their early evolution and subsequent establishment of L1 dominance.

  • 22.
    Suh, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. University of Münster, Institute of Experimental Pathology (ZMBE).
    Bachg, Sandra
    University of Münster, Institute of Experimental Pathology (ZMBE).
    Donnellan, Stephen
    South Australian Museum, Adelaide; The University of Adelaide, School of Biological Sciences.
    Joseph, Leo
    National Research Collections Australia, CSIRO, Australian National Wildlife Collection.
    Brosius, Jürgen
    University of Münster, Institute of Experimental Pathology (ZMBE); Brandenburg Medical School (MHB).
    Kriegs, Jan Ole
    University of Münster, Institute of Experimental Pathology (ZMBE); Westfälisches Landesmuseum mit Planetarium, LWL-Museum für Naturkunde.
    Schmitz, Jürgen
    University of Münster, Institute of Experimental Pathology (ZMBE).
    De-novo emergence of SINE retroposons during the early evolution of passerine birds2017In: Mobile DNA, ISSN 1759-8753, E-ISSN 1759-8753, Vol. 8, article id 21Article in journal (Refereed)
    Abstract [en]

    Background: Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes.

    Results: Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri - songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching.

    Conclusions: We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.

  • 23.
    Suh, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Brosius, Juergen
    Schmitz, Juergen
    Kriegs, Jan Ole
    The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 1791-Article in journal (Refereed)
    Abstract [en]

    Paleovirology involves the identification of ancient endogenous viral elements within eukaryotic genomes. The evolutionary origins of the reverse-transcribing hepatitis B viruses, however, remain elusive, due to the small number of endogenized sequences present in host genomes. Here we report a comprehensively dated genomic record of hepatitis B virus endogenizations that spans bird evolution from > 82 to < 12.1 million years ago. The oldest virus relic extends over a 99% complete hepatitis B virus genome sequence and constitutes the first discovery of a Mesozoic paleovirus genome. We show that Hepadnaviridae are 463 million years older than previously known and provide direct evidence for coexistence of hepatitis B viruses and birds during the Mesozoic and Cenozoic Eras. Finally, phylogenetic analyses and distribution of hepatitis B virus relics suggest that birds potentially are the ancestral hosts of Hepadnaviridae and mammalian hepatitis B viruses probably emerged after a bird-mammal host switch. Our study reveals previously undiscovered and multi-faceted insights into prehistoric hepatitis B virus evolution and provides valuable resources for future studies, such as in-vitro resurrection of Mesozoic hepadnaviruses.

  • 24.
    Suh, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Churakov, Gennady
    Ramakodi, Meganathan P.
    Platt, Roy N., II
    Jurka, Jerzy
    Kojima, Kenji K.
    Caballero, Juan
    Smit, Arian F.
    Vliet, Kent A.
    Hoffmann, Federico G.
    Brosius, Juergen
    Green, Richard E.
    Braun, Edward L.
    Ray, David A.
    Schmitz, Juergen
    Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes2015In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 7, no 1, p. 205-217Article in journal (Refereed)
    Abstract [en]

    Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.

  • 25.
    Suh, Alexander Sang-Jae
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Weber, Claudia C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kehlmaier, Christian
    Braun, Edward L.
    Green, Richard E.
    Fritz, Uwe
    Ray, David A.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Early Mesozoic Coexistence of Amniotes and Hepadnaviridae2014In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, no 12, p. e1004559-Article in journal (Refereed)
    Abstract [en]

    Hepadnaviridae are double-stranded DNA viruses that infect some species of birds and mammals. This includes humans, where hepatitis B viruses (HBVs) are prevalent pathogens in considerable parts of the global population. Recently, endogenized sequences of HBVs (eHBVs) have been discovered in bird genomes where they constitute direct evidence for the coexistence of these viruses and their hosts from the late Mesozoic until present. Nevertheless, virtually nothing is known about the ancient host range of this virus family in other animals. Here we report the first eHBVs from crocodilian, snake, and turtle genomes, including a turtle eHBV that endogenized >207 million years ago. This genomic "fossil'' is >125 million years older than the oldest avian eHBV and provides the first direct evidence that Hepadnaviridae already existed during the Early Mesozoic. This implies that the Mesozoic fossil record of HBV infection spans three of the five major groups of land vertebrates, namely birds, crocodilians, and turtles. We show that the deep phylogenetic relationships of HBVs are largely congruent with the deep phylogeny of their amniote hosts, which suggests an ancient amniote-HBV coexistence and codivergence, at least since the Early Mesozoic. Notably, the organization of overlapping genes as well as the structure of elements involved in viral replication has remained highly conserved among HBVs along that time span, except for the presence of the X gene. We provide multiple lines of evidence that the tumor-promoting X protein of mammalian HBVs lacks a homolog in all other hepadnaviruses and propose a novel scenario for the emergence of X via segmental duplication and overprinting of pre-existing reading frames in the ancestor of mammalian HBVs. Our study reveals an unforeseen host range of prehistoric HBVs and provides novel insights into the genome evolution of hepadnaviruses throughout their long-lasting association with amniote hosts.

  • 26.
    Suh, Alexander
    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.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 1, p. 99-111Article in journal (Refereed)
    Abstract [en]

    Transposable elements (TEs) are genomic parasites capable of inserting virtually anywhere in the host genome, with manifold consequences for gene expression, DNA methylation and genomic stability. Notably, they can contribute to phenotypic variation and hence be associated with, for example, local adaptation and speciation. However, some organisms such as birds have been widely noted for the low densities of TEs in their genomes and this has been attributed to a potential dearth in transposition during their evolution. Here, we show that avian evolution witnessed diverse and abundant transposition on very recent timescales. First, we made an in-depth repeat annotation of the collared flycatcher genome, including identification of 23 new, retrovirus-like LTR retrotransposon families. Then, using whole-genome resequencing data from 200 Ficedula flycatchers, we detected 11,888 polymorphic TE insertions (TE presence/absence variations, TEVs) that segregated within and among species. The density of TEVs was one every 1.5-2.5Mb per individual, with heterozygosities of 0.12-0.16. The majority of TEVs belonged to some 10 different LTR families, most of which are specific to the flycatcher lineage. TEVs were validated by tracing the segregation of hundreds of TEVs across a three-generation pedigree of collared flycatchers and also by their utility as markers recapitulating the phylogenetic relationships among flycatcher species. Our results suggest frequent germline invasions of songbird genomes by novel retroviruses as a rich source of structural variation, which may have had underappreciated phenotypic consequences for the diversification of this species-rich group of birds.

  • 27.
    Suh, Alexander
    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.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds2015In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 13, no 8, article id e1002224Article in journal (Refereed)
    Abstract [en]

    The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS), i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree.

  • 28.
    Suh, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Witt, Christopher C.
    Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA.;Univ New Mexico, Museum Southwestern Biol, Albuquerque, NM 87131 USA..
    Menger, Juliana
    UFZ Helmholtz Ctr Environm Res, Dept Conservat Biol, D-04318 Leipzig, Germany.;Univ Leipzig, Inst Biol, Mol Evolut & Systemat Anim, D-04103 Leipzig, Germany.;INPA, BR-69067375 Manaus, Amazonas, Brazil..
    Sadanandan, Keren R.
    Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore..
    Podsiadlowski, Lars
    Univ Bonn, Inst Evolutionary Biol & Ecol, D-53121 Bonn, Germany..
    Gerth, Michael
    Univ Leipzig, Inst Biol, Mol Evolut & Systemat Anim, D-04103 Leipzig, Germany.;Univ Liverpool, Inst Integrat Biol, Liverpool L69 7ZB, Merseyside, England..
    Weigert, Anne
    Univ Leipzig, Inst Biol, Mol Evolut & Systemat Anim, D-04103 Leipzig, Germany.;Max Planck Inst Evolutionary Anthropol, D-04103 Leipzig, Germany..
    McGuire, Jimmy A.
    Univ Calif Berkeley, Museum Vertebrate Zool, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Mudge, Joann
    Natl Ctr Genome Resources, Santa Fe, NM 87505 USA..
    Edwards, Scott V.
    Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA..
    Rheindt, Frank E.
    Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore..
    Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11396Article in journal (Refereed)
    Abstract [en]

    Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83-99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25-22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20-17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity.

  • 29.
    Talla, Venkat
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kalsoom, Faheema
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dinca, Vlad
    Inst Biol Evolut CSIC UPF, Anim Biodivers & Evolut Program, Barcelona, Spain..
    Vila, Roger
    Inst Biol Evolut CSIC UPF, Anim Biodivers & Evolut Program, Barcelona, Spain..
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wiklund, Christer
    Stockholm Univ, Div Ecol, Dept Zool, Stockholm, Sweden..
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies2017In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 10, p. 2491-2505Article in journal (Refereed)
    Abstract [en]

    Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.

  • 30.
    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.

  • 31.
    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.

  • 32.
    Xu, Luohao
    et al.
    Zhejiang Univ, MOE Lab Biosyst Homeostasis & Protect, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China;Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Auer, Gabriel
    Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Peona, Valentina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Deng, Yuan
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;BGI Shenzhen, Shenzhen, Peoples R China.
    Feng, Shaohong
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;BGI Shenzhen, Shenzhen, Peoples R China.
    Zhang, Guojie
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;Chinese Acad Sci, State Key Lab Genet Resources & Evolut, Kunming Inst Zool, Kunming, Yunnan, Peoples R China;Univ Copenhagen, Sect Ecol & Evolut, Dept Biol, Copenhagen, Denmark.
    Blom, Mozes P. K.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden;Leibniz Inst Evolut & Biodiversitatsforsch, Museum Naturkunde, Berlin, Germany.
    Christidis, Les
    Southern Cross Univ, Natl Marin Sci Ctr, Coffs Harbour, NSW, Australia;Univ Melbourne, Sch Biosci, Victoria, Australia.
    Prost, Stefan
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA;Senckenberg, LOEWE Ctr Translat Biodivers Genom, Frankfurt, Germany.
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    Zhou, Qi
    Zhejiang Univ, MOE Lab Biosyst Homeostasis & Protect, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China;Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds2019In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, no 5, p. 834-844Article in journal (Refereed)
    Abstract [en]

    Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.

1 - 32 of 32
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