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Avian Chromosomal Evolution

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Avian Genomics in Ecology and Evolution

Abstract

An outstanding feature of avian karyotypes is an extraordinary degree of apparent similarity from one species to the next, with the majority of avian species exhibiting 2n = 74–86. Several exceptions to this rule include avian clades that have a large degree of chromosomal fusion and fission. In this chapter we describe patterns of avian chromosomal evolution, including likely associations between karyotype evolution and phenotype. We also describe novel approaches that will facilitate avian chromosome studies at molecular level to unravel the mystery of the significance of this very distinctive genomic structure.

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References

  • Axelsson E, Webster MT, Smith NGC, Burt DW, Ellegren H (2005) Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res 15:120–125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ayala FJ, Coluzzi M (2005) Chromosome speciation: humans, drosophila, and mosquitoes. Proc Natl Acad Sci USA 102(Suppl 1):6535–6542

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Babarinde IA, Saitou N (2016) Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics. Mol Biol Evol 33:1807–1817

    Article  CAS  PubMed  Google Scholar 

  • Baxevanis AD, Ouellette BFF (2004) Bioinformatics: a practical guide to the analysis of genes and proteins. Wiley, New York

    Google Scholar 

  • Beçak ML, Benirschke K, Hsu TC (1971) Chromosome atlas: fish, amphibians, reptiles and birds. Springer, Berlin

    Book  Google Scholar 

  • Bed’hom B, Vaez M, Coville J-L, Gourichon D, Chastel O, Follett S, Burke T, Minvielle F (2012) The lavender plumage colour in Japanese quail is associated with a complex mutation in the region of MLPH that is related to differences in growth, feed consumption and body temperature. BMC Genomics 13:442

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bellott DW, Skaletsky H, Pyntikova T, Mardis ER, Graves T, Kremitzki C, Brown LG, Rozen S, Warren WC, Wilson RK et al (2010) Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature 466:612–616

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Benirschke K, Hsu TC, Becak ML, Becak W, Roberts FL, Shoffner RN, Volpe EP (1973) Chromosome atlas: fish, amphibians, reptiles, and birds. Springer, Berlin

    Google Scholar 

  • Benirschke K, Hsu TC, Becak ML, Becak W, Roberts FL, Shoffner RN, Volpe EP (1975) Chromosome atlas: fish, amphibians, reptiles and birds. Springer, Berlin

    Book  Google Scholar 

  • Brown JH, Hall CAS, Sibly RM (2018) Equal fitness paradigm explained by a trade-off between generation time and energy production rate. Nat Ecol Evol 2:262–268

    Article  PubMed  Google Scholar 

  • Burt DW (2001) Chromosome rearrangement in evolution. eLS. doi: https://doi.org/10.1038/npg.els.0001500

  • Burt DW (2002) Origin and evolution of avian microchromosomes. Cytogenet Genome Res 96:97–112

    Article  CAS  PubMed  Google Scholar 

  • Burt DW, Bruley C, Dunn IC, Jones CT, Ramage A, Law AS, Morrice DR, Paton IR, Smith J, Windsor D et al (1999) The dynamics of chromosome evolution in birds and mammals. Nature 402:411–413

    Article  CAS  PubMed  Google Scholar 

  • Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B et al (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature 513:195–201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carvalho NDM, Arias FJ, da Silva FA, Schneider CH, Gross MC (2015) Cytogenetic analyses of five amazon lizard species of the subfamilies Teiinae and Tupinambinae and review of karyotyped diversity the family Teiidae. Comp Cytogenet 9:625–644

    Article  PubMed  PubMed Central  Google Scholar 

  • Chan JE, Kolodner RD (2011) A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements. PLoS Genet 7:e1002089

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen N, Bellott DW, Page DC, Clark AG (2012) Identification of avian W-linked contigs by short-read sequencing. BMC Genomics 13:183

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen S, Krinsky BH, Long M (2013) New genes as drivers of phenotypic evolution. Nat Rev Genet 14:645–660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christidis L (1990) Aves. In: John B et al (eds) Animal cytogenetics. Volume 4: Chordata 3 B. Gebrüder Borntraeger, Berlin

    Google Scholar 

  • Clarke J, Wu H-C, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nano 4:265–270

    Article  CAS  Google Scholar 

  • Coyle S, Kroll E (2008) Starvation induces genomic rearrangements and starvation-resilient phenotypes in yeast. Mol Biol Evol 25:310–318

    Article  CAS  PubMed  Google Scholar 

  • Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ, Mandawala A, Fowler K, Joseph S, Swain MT, Griffin DK et al (2017) Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res 27:875–884

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Davis JK, Mittel LB, Lowman JJ, Thomas PJ, Maney DL, Martin CL, Thomas JW (2011) Haplotype-based genomic sequencing of a chromosomal polymorphism in the white-throated sparrow (Zonotrichia albicollis). J Hered 102:380–390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Oliveira EH, Habermann FA, Lacerda O, Sbalqueiro IJ, Wienberg J, Muller S (2005) Chromosome reshuffling in birds of prey: the karyotype of the world’s largest eagle (Harpy eagle, Harpia harpyja) compared to that of the chicken (Gallus gallus). Chromosoma 114:338–343

    Article  PubMed  Google Scholar 

  • De Smet WHO (1981) The nuclear Feulgen-DNA content of the vertebrates (especially reptiles), with notes on the cell and chromosome size. Acta Zool Pathol Antverp 76:119–167

    Google Scholar 

  • Deakin JE, Ezaz T (2014) Tracing the evolution of amniote chromosomes. Chromosoma 123:201–216

    Article  PubMed  PubMed Central  Google Scholar 

  • Delany ME, Gessaro TM, Rodrigue KL, Daniels LM (2007) Chromosomal mapping of chicken mega-telomere arrays to GGA9, 16, 28 and W using a cytogenomic approach. Cytogenet Genome Res 117:54–63

    Article  CAS  PubMed  Google Scholar 

  • Derjusheva S, Kurganova A, Habermann F, Gaginskaya E (2004) High chromosome conservation detected by comparative chromosome painting in chicken, pigeon and passerine birds. Chromosom Res 12:715–723

    Article  CAS  Google Scholar 

  • Dodgson JB, Delany ME, Cheng HH (2011) Poultry genome sequences: progress and outstanding challenges. Cytogenet Genome Res 134:19–26

    Article  CAS  PubMed  Google Scholar 

  • Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D (2002) Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 99:16144–16149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    Article  CAS  PubMed  Google Scholar 

  • Ellegren H (2010) Evolutionary stasis: the stable chromosomes of birds. Trends Ecol Evol 25:283–291

    Article  PubMed  Google Scholar 

  • Ezaz T, Srikulnath K, Graves JA (2017) Origin of amniote sex chromosomes: an ancestral super-sex chromosome, or common requirements? J Hered 108:94–105

    Article  CAS  PubMed  Google Scholar 

  • Farré M, Bosch M, López-Giráldez F, Ponsà M, Ruiz-Herrera A (2011) Assessing the role of tandem repeats in shaping the genomic architecture of great apes. PLoS One 6:e27239

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Farré M, Narayan J, Slavov GT, Damas J, Auvil L, Li C, Jarvis ED, Burt DW, Griffin DK, Larkin DM (2016) Novel insights into chromosome evolution in birds, archosaurs, and reptiles. Genome Biol Evol 8:2442–2451

    Article  PubMed  PubMed Central  Google Scholar 

  • Graphodatsky AS, Trifonov VA, Stanyon R (2011) The genome diversity and karyotype evolution of mammals. Mol Cytogenet 4:22

    Article  PubMed  PubMed Central  Google Scholar 

  • Graves JA (2013) How to evolve new vertebrate sex determining genes. Dev Dyn 242:354–359

    Article  PubMed  CAS  Google Scholar 

  • Graves JA (2014) Avian sex, sex chromosomes, and dosage compensation in the age of genomics. Chromosom Res 22:45–57

    Article  CAS  Google Scholar 

  • Gregory TR (2002) A bird’s-eye view of the c-value enigma: genome size, cell size, and metabolic rate in the class aves. Evolution 56:121–130

    Article  CAS  PubMed  Google Scholar 

  • Gregory TR (2005) The evolution of the genome. Elsevier Academic, Burlington, MA

    Google Scholar 

  • Gregory TR (2017) Animal genome size database

    Google Scholar 

  • Gregory TR, Andrews CB, McGuire JA, Witt CC (2009) The smallest avian genomes are found in hummingbirds. Proc R Soc B Biol Sci 276:3753–3757. https://doi.org/10.1098/rspb.2009.1004

    Article  CAS  Google Scholar 

  • Griffin DK, Haberman F, Masabanda J, O'Brien P, Bagga M, Sazanov A, Smith J, Burt DW, Ferguson-Smith M, Wienberg J (1999) Micro- and macrochromosome paints generated by flow cytometry and microdissection: tools for mapping the chicken genome. Cytogenet Cell Genet 87:278

    Article  CAS  PubMed  Google Scholar 

  • Griffin DK, Robertson LB, Tempest HG, Skinner BM (2007) The evolution of the avian genome as revealed by comparative molecular cytogenetics. Cytogenet Genome Res 117:64–77

    Article  CAS  PubMed  Google Scholar 

  • Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ et al (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393–398

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guttenbach M, Nanda I, Feichtinger W, Masabanda JS, Griffin DK, Schmid M (2003) Comparative chromosome painting of chicken autosomal paints 1–9 in nine different bird species. Cytogenet Genome Res 103:173–184

    Article  CAS  PubMed  Google Scholar 

  • Habermann FA, Cremer M, Walter J, Kreth G, von Hase J, Bauer K, Wienberg J, Cremer C, Cremer T, Solovei I (2001) Arrangements of macro- and microchromosomes in chicken cells. Chromosom Res 9:569–584

    Article  CAS  Google Scholar 

  • Hansmann T, Nanda I, Volobouev V, Yang F, Schartl M, Haaf T, Schmid M (2009) Cross-species chromosome painting corroborates microchromosome fusion during karyotype evolution of birds. Cytogenet Genome Res 126:281–304

    Article  CAS  PubMed  Google Scholar 

  • Harewood L, Fraser P (2014) The impact of chromosomal rearrangements on regulation of gene expression. Hum Mol Genet 23:R76–R82

    Article  CAS  PubMed  Google Scholar 

  • Hughes AL, Friedman R (2008) Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes. Mol Biol Evol 25:2681–2688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Itoh Y, Arnold AP (2005) Chromosomal polymorphism and comparative painting analysis in the zebra finch. Chromosom Res 13:47–56

    Article  CAS  Google Scholar 

  • Itoh Y, Kampf K, Balakrishnan CN, Arnold AP (2011) Karyotypic polymorphism of the zebra finch Z chromosome. Chromosoma 120:255–264

    Article  PubMed  PubMed Central  Google Scholar 

  • Jones BR, Rajaraman A, Tannier E, Chauve C (2012) ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics (Oxford, England) 28:2388–2390

    Article  CAS  Google Scholar 

  • Kapusta A, Suh A (2017) Evolution of bird genomes—a transposon’s-eye view. Ann N Y Acad Sci 1389:164–185

    Article  PubMed  Google Scholar 

  • Kasai F, O'Brien PC, Martin S, Ferguson-Smith MA (2012) Extensive homology of chicken macrochromosomes in the karyotypes of Trachemys scripta elegans and Crocodylus niloticus revealed by chromosome painting despite long divergence times. Cytogenet Genome Res 136:303–307

    Article  CAS  PubMed  Google Scholar 

  • Kawai A, Ishijima J, Nishida C, Kosaka A, Ota H, Kohno S, Matsuda Y (2009) The ZW sex chromosomes of Gekko hokouensis (Gekkonidae, Squamata) represent highly conserved homology with those of avian species. Chromosoma 118:43–51

    Article  PubMed  Google Scholar 

  • Kim J, Farré M, Auvil L, Capitanu B, Larkin DM, Ma J, Lewin HA (2017) Reconstruction and evolutionary history of eutherian chromosomes. Proc Natl Acad Sci 114:E5379–E5388

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim J, Larkin DM, Cai Q, Asan ZY, Ge R-L, Auvil L, Capitanu B, Zhang G, Lewin HA et al (2013) Reference-assisted chromosome assembly. Proc Natl Acad Sci 110:1785–1790

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane T, Thybert D et al (2016) Chromosome assembly of large and complex genomes using multiple references. bioRxiv. https://doi.org/10.1101/088435

  • Kolmogorov M, Raney B, Paten B, Pham S (2014) Ragout—a reference-assisted assembly tool for bacterial genomes. Bioinformatics (Oxford, England) 30:i302–i309

    Article  CAS  Google Scholar 

  • Korlach J, Gedman G, Kingan SB, Chin CS, Howard JT, Audet JN, Cantin L, Jarvis ED (2017) De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. GigaScience 6:1–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kupper C, Stocks M, Risse JE, Dos Remedios N, Farrell LL, McRae SB, Morgan TC, Karlionova N, Pinchuk P, Verkuil YI et al (2016) A supergene determines highly divergent male reproductive morphs in the ruff. Nat Genet 48:79–83

    Article  CAS  PubMed  Google Scholar 

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    Article  CAS  PubMed  Google Scholar 

  • Ledesma M, Freitas T, Da Silva J, Da Silva F, Gunski R (2003) Descripción cariotípica de Spheniscus magellanicus (Spheniscidae). Hornero 18:61–64

    Google Scholar 

  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E et al (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478:476–482

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lithgow PE, O'Connor R, Smith D, Fonseka G, Al Mutery A, Rathje C, Frodsham R, O'Brien P, Kasai F, Ferguson-Smith MA et al (2014) Novel tools for characterising inter and intra chromosomal rearrangements in avian microchromosomes. Chromosom Res 22:85–97

    CAS  Google Scholar 

  • Lovell PV, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, Warren WC, Mello CV (2014) Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol 15:565

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lynch M (2007) The origins of genome architecture. Sinauer Associates, Sunderland, MA

    Google Scholar 

  • Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W (2006) Reconstructing contiguous regions of an ancestral genome. Genome Res 16:1557–1565

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mak ACY, Lai YYY, Lam ET, Kwok T-P, Leung AKY, Poon A, Mostovoy Y, Hastie AR, Stedman W, Anantharaman T et al (2016) Genome-wide structural variation detection by genome mapping on nanochannel arrays. Genetics 202:351–362

    Article  CAS  PubMed  Google Scholar 

  • Masabanda JS, Burt DW, O’Brien PCM, Vignal A, Fillon V, Walsh PS, Cox H, Tempest HG, Smith J, Habermann F et al (2004) Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype. Genetics 166:1367–1373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matsubara K, Tarui H, Toriba M, Yamada K, Nishida-Umehara C, Agata K, Matsuda Y (2006) Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes. Proc Natl Acad Sci 103:18190–18195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matsuda Y, Nishida-Umehara C, Tarui H, Kuroiwa A, Yamada K, Isobe T, Ando J, Fujiwara A, Hirao Y, Nishimura O et al (2005) Highly conserved linkage homology between birds and turtles: bird and turtle chromosomes are precise counterparts of each other. Chromosom Res 13:601–615

    Article  CAS  Google Scholar 

  • Moore JK, Haber JE (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 16:2164–2173

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L et al (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613–617

    Article  CAS  PubMed  Google Scholar 

  • Nam K, Mugal C, Nabholz B, Schielzeth H, Wolf JB, Backstrom N, Kunstner A, Balakrishnan CN, Heger A, Ponting CP et al (2010) Molecular evolution of genes in avian genomes. Genome Biol 11:R68

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nanda I, Benisch P, Fetting D, Haaf T, Schmid M (2011) Synteny conservation of chicken macrochromosomes 1-10 in different avian lineages revealed by cross-species chromosome painting. Cytogenet Genome Res 132:165–181

    Article  CAS  PubMed  Google Scholar 

  • Nanda I, Karl E, Griffin DK, Schartl M, Schmid M (2007) Chromosome repatterning in three representative parrots (Psittaciformes) inferred from comparative chromosome painting. Cytogenet Genome Res 117:43–53

    Article  CAS  PubMed  Google Scholar 

  • Nanda I, Shan Z, Schartl M, Burt DW, Koehler M, Nothwang H-G, Grutzner F, Paton IR, Windsor D, Dunn I et al (1999) 300 million years of conserved synteny between chicken Z and human chromosome 9. Nat Genet 21:258–259

    Article  CAS  PubMed  Google Scholar 

  • Nie W, O’Brien PC, Ng BL, Fu B, Volobouev V, Carter NP, Ferguson-Smith MA, Yang F (2009) Avian comparative genomics: reciprocal chromosome painting between domestic chicken (Gallus gallus) and the stone curlew (Burhinus oedicnemus, Charadriiformes)—an atypical species with low diploid number. Chromosom Res 17:99–113

    Article  CAS  Google Scholar 

  • Nishida C, Ishijima J, Kosaka A, Tanabe H, Habermann FA, Griffin DK, Matsuda Y (2008) Characterization of chromosome structures of Falconinae (Falconidae, Falconiformes, Aves) by chromosome painting and delineation of chromosome rearrangements during their differentiation. Chromosom Res 16:171–181

    Article  CAS  Google Scholar 

  • O’Hare TH, Delany ME (2009) Genetic variation exists for telomeric array organization within and among the genomes of normal, immortalized, and transformed chicken systems. Chromosom Res 17:947–964

    Article  CAS  Google Scholar 

  • O'Meally D, Ezaz T, Georges A, Sarre SD, Graves JA (2012) Are some chromosomes particularly good at sex? Insights from amniotes. Chromosom Res 20:7–19

    Article  CAS  Google Scholar 

  • Olmo E (2008) Trends in the evolution of reptilian chromosomes. Integr Comp Biol 48:486–493

    Article  PubMed  Google Scholar 

  • Organ CL, Moreno RG, Edwards SV (2008) Three tiers of genome evolution in reptiles. Integr Comp Biol 48:494–504

    Article  PubMed  PubMed Central  Google Scholar 

  • Organ CL, Shedlock AM, Meade A, Pagel M, Edwards SV (2007) Origin of avian genome size and structure in non-avian dinosaurs. Nature 446:180–184

    Article  CAS  PubMed  Google Scholar 

  • Pigozzi MI (2016) The chromosomes of birds during meiosis. Cytogenet Genome Res 150:128–138

    Article  PubMed  CAS  Google Scholar 

  • Pokorna M, Giovannotti M, Kratochvil L, Caputo V, Olmo E, Ferguson-Smith MA, Rens W (2012) Conservation of chromosomes syntenic with avian autosomes in squamate reptiles revealed by comparative chromosome painting. Chromosoma 121:409–418

    Article  CAS  PubMed  Google Scholar 

  • Puerma E, Orengo DJ, Aguadé M (2016) The origin of chromosomal inversions as a source of segmental duplications in the Sophophora subgenus of Drosophila. Sci Rep 6:30715

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW et al (2016) Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 26:342–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raudsepp T, Houck ML, O'Brien PC, Ferguson-Smith MA, Ryder OA, Chowdhary BP (2002) Cytogenetic analysis of California condor (Gymnogyps californianus) chromosomes: comparison with chicken (Gallus gallus) macrochromosomes. Cytogenet Genome Res 98:54–60

    Article  CAS  PubMed  Google Scholar 

  • Richards MP (2003) Genetic regulation of feed intake and energy balance in poultry. Poult Sci 82:907–916

    Article  CAS  PubMed  Google Scholar 

  • Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O’Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C et al (2014) Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 15:1–18

    Article  Google Scholar 

  • Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP et al (2005) The DNA sequence of the human X chromosome. Nature 434:325–337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rutkowska J, Lagisz M, Nakagawa S (2012) The long and the short of avian W chromosomes: no evidence for gradual W shortening. Biol Lett 8:636–638

    Article  PubMed  PubMed Central  Google Scholar 

  • Scanes CG (2014) Sturkie’s avian physiology. Elsevier Science, Amsterdam

    Google Scholar 

  • Segura J, Ferretti L, Ramos-Onsins S, Capilla L, Farré M, Reis F, Oliver-Bonet M, Fernández-Bellón H, Garcia F, Garcia-Caldés M et al (2013) Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference. Proc R Soc B Biol Sci 280:20131945

    Article  Google Scholar 

  • Shang WH, Hori T, Toyoda A, Kato J, Popendorf K, Sakakibara Y, Fujiyama A, Fukagawa T (2010) Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences. Genome Res 20:1219–1228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shetty S, Griffin DK, Graves JA (1999) Comparative painting reveals strong chromosome homology over 80 million years of bird evolution. Chromosom Res 7:289–295

    Article  CAS  Google Scholar 

  • Shibusawa M, Nishida-Umehara C, Masabanda J, Griffin DK, Isobe T, Matsuda Y (2002) Chromosome rearrangements between chicken and guinea fowl defined by comparative chromosome painting and FISH mapping of DNA clones. Cytogenet Genome Res 98:225–230

    Article  CAS  PubMed  Google Scholar 

  • Shields GF, Jarell GH, Redrupp E (1982) Enlarged sex chromosomes of woodpeckers (Piciformes). Auk 99:767–771

    Google Scholar 

  • Skinner BM, Griffin DK (2012) Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints. Heredity (Edinb) 108:37–41

    Article  CAS  Google Scholar 

  • Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A, Nater A, Bureš S, Garamszegi LZ, Hogner S et al (2015) Evolutionary analysis of the female-specific avian W chromosome. Nat Commun 6:7330

    Article  CAS  PubMed  Google Scholar 

  • Smith CA, Roeszler KN, Ohnesorg T, Cummins DM, Farlie PG, Doran TJ, Sinclair AH (2009) The avian Z-linked gene DMRT1 is required for male sex determination in the chicken. Nature 461:267–271

    Article  CAS  PubMed  Google Scholar 

  • Smith E, Shi L, Drummond P, Rodriguez L, Hamilton R, Powell E, Nahashon S, Ramlal S, Smith G, Foster J (2000) Development and characterization of expressed sequence tags for the turkey (Meleagris gallopavo) genome and comparative sequence analysis with other birds. Anim Genet 31:62–67

    Article  CAS  PubMed  Google Scholar 

  • Thomas JW, Cáceres M, Lowman JJ, Morehouse CB, Short ME, Baldwin EL, Maney DL, Martin CL (2008) The chromosomal polymorphism linked to variation in social behavior in the white-throated sparrow (Zonotrichia albicollis) is a complex rearrangement and suppressor of recombination. Genetics 179:1455–1468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tiersch TR, Wachtel SS (1991) On the evolution of genome size of birds. J Hered 82:363–368

    Article  CAS  PubMed  Google Scholar 

  • Tomaszkiewicz M, Medvedev P, Makova KD (2017) Y and W chromosome assemblies: approaches and discoveries. Trends Genet 33:266–282

    Article  CAS  PubMed  Google Scholar 

  • Tuiskula-Haavisto M, Honkatukia M, Vilkki J, de Koning DJ, Schulman NF, Maki-Tanila A (2002) Mapping of quantitative trait loci affecting quality and production traits in egg layers. Poult Sci 81:919–927

    Article  CAS  PubMed  Google Scholar 

  • Ullastres A, Farré M, Capilla L, Ruiz-Herrera A (2014) Unraveling the effect of genomic structural changes in the rhesus macaque—implications for the adaptive role of inversions. BMC Genomics 15:530

    Article  PubMed  PubMed Central  Google Scholar 

  • Uno Y, Nishida C, Tarui H, Ishishita S, Takagi C, Nishimura O, Ishijima J, Ota H, Kosaka A, Matsubara K et al (2012) Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping. PLoS One 7:e53027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Venturini G, D'Ambrogi R, Capanna E (1986) Size and structure of the bird genome—I. DNA content of 48 species of Neognathae. Comp Biochem Physiol B Comp Biochem 85:61–65

    Article  CAS  Google Scholar 

  • Volker M, Backstrom N, Skinner BM, Langley EJ, Bunzey SK, Ellegren H, Griffin DK (2010) Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Res 20:503–511

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry RJ, Basa S, Walker JA, Smith JJ (2011) Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res 21:1306–1312

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F et al (2016) A new chicken genome assembly provides insight into avian genome structure. G3: Genes|Genomes|Genetics 7:109–117. https://doi.org/10.1534/g3.116.035923

    Article  CAS  PubMed Central  Google Scholar 

  • Wessler SR (2006) Transposable elements and the evolution of eukaryotic genomes. Proc Natl Acad Sci 103:17600–17601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K et al (2004) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3:e7

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wright NA, Gregory TR, Witt CC (2014) Metabolic ‘engines’ of flight drive genome size reduction in birds. Proc R Soc B Biol Sci 281:20132780

    Article  Google Scholar 

  • Wurster DH, Benirschke K (1970) Indian Muntjac, Muntiacus muntiak: a deer with a low diploid chromosome number. Science 168:1364–1366

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Cowled C, Shi Z, Huang Z, Bishop-Lilly KA, Fang X, Wynne JW, Xiong Z, Baker ML, Zhao W et al (2013) Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science 339:456–460

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW et al (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science (New York, NY) 346:1311–1320

    Article  CAS  Google Scholar 

  • Zhang J, Li C, Zhou Q, Zhang G (2015) Improving the ostrich genome assembly using optical mapping data. GigaScience 4:24

    PubMed  PubMed Central  Google Scholar 

  • Zheng GXY, Lau BT, Schnall-Levin M, Jarosz M, Bell JM, Hindson CM, Kyriazopoulou-Panagiotopoulou S, Masquelier DA, Merrill L, Terry JM et al (2016) Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nat Biotech 34:303–311

    Article  CAS  Google Scholar 

  • Zinzow-Kramer WM, Horton BM, McKee CD, Michaud JM, Tharp GK, Thomas JW, Tuttle EM, Yi S, Maney DL (2015) Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows. Genes Brain Behav 14:641–654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zlotina A, Galkina S, Krasikova A, Crooijmans RP, Groenen MA, Gaginskaya E, Deryusheva S (2012) Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions. Chromosom Res 20:1017–1032

    Article  CAS  Google Scholar 

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Damas, J., O’Connor, R.E., Griffin, D.K., Larkin, D.M. (2019). Avian Chromosomal Evolution. In: Kraus, R. (eds) Avian Genomics in Ecology and Evolution. Springer, Cham. https://doi.org/10.1007/978-3-030-16477-5_4

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