Evolutionary Biology

A bird’s white-eye view on avian sex chromosome evolution

10.24072/pcjournal.70 - Peer Community Journal, Volume 1 (2021), article no. e63.

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Chromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. Here, we took advantage of this unusual event to study the early stages of sex chromosome evolution. To do so, we sequenced a female (ZW) of two Sylvioidea species, a Zosterops borbonicus and a Z. pallidus. Then, we organized the Z. borbonicus scaffolds along chromosomes and annotated genes. Molecular phylogenetic dating under various methods and calibration sets confidently confirmed the recent diversification of the genus Zosterops (1-3.5 million years ago), thus representing one of the most exceptional rates of diversification among vertebrates. We then combined genomic coverage comparisons of five males and seven females, and homology with the zebra finch genome (Taeniopygia guttata) to identify sex chromosome scaffolds, as well as the candidate chromosome breakpoints for the two translocation events. We observed reduced levels of within-species diversity in both translocated regions and, as expected, even more so on the neoW chromosome. In order to compare the rates of molecular evolution in genomic regions of the autosomal-to-sex transitions, we then estimated the ratios of non-synonymous to synonymous polymorphisms (N/S) and substitutions (dN/dS). Based on both ratios, no or little contrast between autosomal and Z genes was observed, thus representing a very different outcome than the higher ratios observed at the neoW genes. In addition, we report significant changes in base composition content for translocated regions on the W and Z chromosomes and a large accumulation of transposable elements (TE) on the newly W region. Our results revealed contrasted signals of molecular evolution changes associated to these autosome-to-sex transitions, with congruent signals of a W chromosome degeneration yet a surprisingly weak support for a fast-Z effect.

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DOI: 10.24072/pcjournal.70
Leroy, Thibault 1; Anselmetti, Yoann 1; Tilak, Marie-Ka 1; Bérard, Sèverine 1; Csukonyi, Laura 1, 2; Gabrielli, Maëva 2; Scornavacca, Céline 1; Milá, Borja 3; Thébaud, Christophe 2; Nabholz, Benoit 1

1 ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
2 Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174 CNRS – Université Paul Sabatier – IRD, Toulouse, France
3 National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
     author = {Leroy, Thibault and Anselmetti, Yoann and Tilak, Marie-Ka and B\'erard, S\`everine and Csukonyi, Laura and Gabrielli, Ma\"eva and Scornavacca, C\'eline and Mil\'a, Borja and Th\'ebaud, Christophe and Nabholz, Benoit},
     title = {A bird{\textquoteright}s white-eye view on avian sex chromosome evolution},
     journal = {Peer Community Journal},
     eid = {e63},
     publisher = {Peer Community In},
     volume = {1},
     year = {2021},
     doi = {10.24072/pcjournal.70},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.70/}
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Leroy, Thibault; Anselmetti, Yoann; Tilak, Marie-Ka; Bérard, Sèverine; Csukonyi, Laura; Gabrielli, Maëva; Scornavacca, Céline; Milá, Borja; Thébaud, Christophe; Nabholz, Benoit. A bird’s white-eye view on avian sex chromosome evolution. Peer Community Journal, Volume 1 (2021), article  no. e63. doi : 10.24072/pcjournal.70. https://peercommunityjournal.org/articles/10.24072/pcjournal.70/

Peer reviewed and recommended by PCI : 10.24072/pci.evolbiol.100073

[1] Abascal, F.; Zardoya, R.; Telford, M. J. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations, Nucleic Acids Research, Volume 38 (2010) no. suppl_2 | Article

[2] Amemiya, C. T.; Alföldi, J.; Lee, A. P.; Fan, S.; Philippe, H.; MacCallum, I.; Braasch, I.; Manousaki, T.; Schneider, I.; Rohner, N.; Organ, C.; Chalopin, D.; Smith, J. J.; Robinson, M.; Dorrington, R. A.; Gerdol, M.; Aken, B.; Biscotti, M. A.; Barucca, M.; Baurain, D.; Berlin, A. M.; Blatch, G. L.; Buonocore, F.; Burmester, T.; Campbell, M. S.; Canapa, A.; Cannon, J. P.; Christoffels, A.; De Moro, G.; Edkins, A. L.; Fan, L.; Fausto, A. M.; Feiner, N.; Forconi, M.; Gamieldien, J.; Gnerre, S.; Gnirke, A.; Goldstone, J. V.; Haerty, W.; Hahn, M. E.; Hesse, U.; Hoffmann, S.; Johnson, J.; Karchner, S. I.; Kuraku, S.; Lara, M.; Levin, J. Z.; Litman, G. W.; Mauceli, E.; Miyake, T.; Mueller, M. G.; Nelson, D. R.; Nitsche, A.; Olmo, E.; Ota, T.; Pallavicini, A.; Panji, S.; Picone, B.; Ponting, C. P.; Prohaska, S. J.; Przybylski, D.; Saha, N. R.; Ravi, V.; Ribeiro, F. J.; Sauka-Spengler, T.; Scapigliati, G.; Searle, S. M. J.; Sharpe, T.; Simakov, O.; Stadler, P. F.; Stegeman, J. J.; Sumiyama, K.; Tabbaa, D.; Tafer, H.; Turner-Maier, J.; van Heusden, P.; White, S.; Williams, L.; Yandell, M.; Brinkmann, H.; Volff, J.-N.; Tabin, C. J.; Shubin, N.; Schartl, M.; Jaffe, D. B.; Postlethwait, J. H.; Venkatesh, B.; Di Palma, F.; Lander, E. S.; Meyer, A.; Lindblad-Toh, K. The African coelacanth genome provides insights into tetrapod evolution, Nature, Volume 496 (2013) no. 7445, pp. 311-316 | Article

[3] Anselmetti, Y.; Duchemin, W.; Tannier, E.; Chauve, C.; Bérard, S. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes, BMC Genomics, Volume 19 (2018) no. S2 | Article

[4] Bachtrog, D. Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila, Genome Research, Volume 15 (2005) no. 10, pp. 1393-1401 | Article

[5] Bachtrog, D.; Charlesworth, B. Reduced adaptation of a non-recombining neo-Y chromosome, Nature, Volume 416 (2002) no. 6878, pp. 323-326 | Article

[6] Backström, N.; Forstmeier, W.; Schielzeth, H.; Mellenius, H.; Nam, K.; Bolund, E.; Webster, M. T.; Öst, T.; Schneider, M.; Kempenaers, B.; Ellegren, H. The recombination landscape of the zebra finch Taeniopygia guttata genome, Genome Research, Volume 20 (2010) no. 4, pp. 485-495 | Article

[7] Benton M, ; Donoghue P, ; Asher R J, Calibrating and constraining molecular clocks. In: The timetree of Life ((2009)), pp. 35-86

[8] Backström, N.; Forstmeier, W.; Schielzeth, H.; Mellenius, H.; Nam, K.; Bolund, E.; Webster, M. T.; Öst, T.; Schneider, M.; Kempenaers, B.; Ellegren, H. The recombination landscape of the zebra finch Taeniopygia guttata genome, Genome Research, Volume 20 (2010) no. 4, pp. 485-495 | Article

[9] Boetzer, M.; Pirovano, W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information, BMC Bioinformatics, Volume 15 (2014) no. 1 | Article

[10] Boles, W. E. Fossil Songbirds (Passeriformes) from the Early Eocene of Australia, Emu - Austral Ornithology, Volume 97 (1997) no. 1, pp. 43-50 | Article

[11] Bolger, A. M.; Lohse, M.; Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, Volume 30 (2014) no. 15, pp. 2114-2120 | Article

[12] Botero-Castro, F.; Figuet, E.; Tilak, M.-K.; Nabholz, B.; Galtier, N. Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds, Molecular Biology and Evolution, Volume 34 (2017) no. 12, pp. 3123-3131 | Article

[13] Bourgeois, Y. X. C.; Delahaie, B.; Gautier, M.; Lhuillier, E.; Malé, P.-J. G.; Bertrand, J. A. M.; Cornuault, J.; Wakamatsu, K.; Bouchez, O.; Mould, C.; Bruxaux, J.; Holota, H.; Milá, B.; Thébaud, C. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird, Royal Society Open Science, Volume 4 (2017) no. 2 | Article

[14] Bourgeois, Y.; Ruggiero, R. P.; Manthey, J. D.; Boissinot, S. Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis, Genome Biology and Evolution, Volume 11 (2019) no. 7, pp. 2009-2022 | Article

[15] Bracewell, R. R.; Bentz, B. J.; Sullivan, B. T.; Good, J. M. Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest, Nature Communications, Volume 8 (2017) no. 1 | Article

[16] Bradnam, K. R.; Fass, J. N.; Alexandrov, A.; Baranay, P.; Bechner, M.; Birol, I.; Boisvert, S.; Chapman, J. A.; Chapuis, G.; Chikhi, R.; Chitsaz, H.; Chou, W.-C.; Corbeil, J.; Del Fabbro, C.; Docking, T. R.; Durbin, R.; Earl, D.; Emrich, S.; Fedotov, P.; Fonseca, N. A.; Ganapathy, G.; Gibbs, R. A.; Gnerre, S.; Godzaridis, É.; Goldstein, S.; Haimel, M.; Hall, G.; Haussler, D.; Hiatt, J. B.; Ho, I. Y.; Howard, J.; Hunt, M.; Jackman, S. D.; Jaffe, D. B.; Jarvis, E. D.; Jiang, H.; Kazakov, S.; Kersey, P. J.; Kitzman, J. O.; Knight, J. R.; Koren, S.; Lam, T.-W.; Lavenier, D.; Laviolette, F.; Li, Y.; Li, Z.; Liu, B.; Liu, Y.; Luo, R.; MacCallum, I.; MacManes, M. D.; Maillet, N.; Melnikov, S.; Naquin, D.; Ning, Z.; Otto, T. D.; Paten, B.; Paulo, O. S.; Phillippy, A. M.; Pina-Martins, F.; Place, M.; Przybylski, D.; Qin, X.; Qu, C.; Ribeiro, F. J.; Richards, S.; Rokhsar, D. S.; Ruby, J. G.; Scalabrin, S.; Schatz, M. C.; Schwartz, D. C.; Sergushichev, A.; Sharpe, T.; Shaw, T. I.; Shendure, J.; Shi, Y.; Simpson, J. T.; Song, H.; Tsarev, F.; Vezzi, F.; Vicedomini, R.; Vieira, B. M.; Wang, J.; Worley, K. C.; Yin, S.; Yiu, S.-M.; Yuan, J.; Zhang, G.; Zhang, H.; Zhou, S.; Korf, I. F. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, GigaScience, Volume 2 (2013) no. 1 | Article

[17] Brooke, M. d. L.; Welbergen, J. A.; Mainwaring, M. C.; van der Velde, M.; Harts, A. M. F.; Komdeur, J.; Amos, W. Widespread Translocation from Autosomes to Sex Chromosomes Preserves Genetic Variability in an Endangered Lark, Journal of Molecular Evolution, Volume 70 (2010) no. 3, pp. 242-246 | Article

[18] Cai, T.; Cibois, A.; Alström, P.; Moyle, R. G.; Kennedy, J. D.; Shao, S.; Zhang, R.; Irestedt, M.; Ericson, P. G.; Gelang, M.; Qu, Y.; Lei, F.; Fjeldså, J. Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes), Molecular Phylogenetics and Evolution, Volume 130 (2019), pp. 346-356 | Article

[19] Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, Volume 25 (2009) no. 15, pp. 1972-1973 | Article

[20] Charlesworth, B. The Evolution of Sex Chromosomes, Science, Volume 251 (1991) no. 4997, pp. 1030-1033 | Article

[21] Charlesworth, B.; Charlesworth, D. Rapid fixation of deleterious alleles can be caused by Muller's ratchet, Genetical Research, Volume 70 (1997) no. 1, pp. 63-73 | Article

[22] Charlesworth, B.; Charlesworth, D. The degeneration of Y chromosomes, Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Volume 355 (2000) no. 1403, pp. 1563-1572 | Article

[23] Charlesworth, B.; Sniegowski, P.; Stephan, W. The evolutionary dynamics of repetitive DNA in eukaryotes, Nature, Volume 371 (1994) no. 6494, pp. 215-220 | Article

[24] Clegg, S. M.; Phillimore, A. B. The influence of gene flow and drift on genetic and phenotypic divergence in two species ofZosteropsin Vanuatu, Philosophical Transactions of the Royal Society B: Biological Sciences, Volume 365 (2010) no. 1543, pp. 1077-1092 | Article

[25] Coghlan, A.; Eichler, E. E.; Oliver, S. G.; Paterson, A. H.; Stein, L. Chromosome evolution in eukaryotes: a multi-kingdom perspective, Trends in Genetics, Volume 21 (2005) no. 12, pp. 673-682 | Article

[26] Cornetti, L.; Valente, L. M.; Dunning, L. T.; Quan, X.; Black, R. A.; Hébert, O.; Savolainen, V. The Genome of the “Great Speciator” Provides Insights into Bird Diversification, Genome Biology and Evolution, Volume 7 (2015) no. 9, pp. 2680-2691 | Article

[27] Cornuault, J.; Delahaie, B.; Bertrand, J. A. M.; Bourgeois, Y. X. C.; Milá, B.; Heeb, P.; Thébaud, C. Morphological and plumage colour variation in the Réunion grey white-eye (Aves:Zosterops borbonicus): assessing the role of selection, Biological Journal of the Linnean Society, Volume 114 (2014) no. 2, pp. 459-473 | Article

[28] Davis, J. K.; Thomas, P. J.; Thomas, J. W. A W-linked palindrome and gene conversion in New World sparrows and blackbirds, Chromosome Research, Volume 18 (2010) no. 5, pp. 543-553 | Article

[29] Delahaie, B.; Cornuault, J.; Masson, C.; Bertrand, J. A. M.; Bourgeois, Y. X. C.; Milá, B.; Thébaud, C. Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex, Journal of Evolutionary Biology, Volume 30 (2017) no. 12, pp. 2132-2145 | Article

[30] Derryberry, E. P.; Claramunt, S.; Derryberry, G.; Chesser, R. T.; Cracraft, J.; Aleixo, A.; Pérez-Emán, J.; Remsen Jr., J. V.; Brumfield, R. T. Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (Aves: Furnariidae), Evolution, Volume 65 (2011) no. 10, pp. 2973-2986 | Article

[31] Diamond, J. M.; Gilpin, M. E.; Mayr, E. Species-distance relation for birds of the Solomon Archipelago, and the paradox of the great speciators, Proceedings of the National Academy of Sciences, Volume 73 (1976) no. 6, pp. 2160-2164 | Article

[32] Dierickx, E. G.; Sin, S. Y. W.; van Veelen, H. P. J.; Brooke, M. d. L.; Liu, Y.; Edwards, S. V.; Martin, S. H. Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark, Proceedings of the Royal Society B: Biological Sciences, Volume 287 (2020) no. 1922 | Article

[33] Drummond, D. A.; Wilke, C. O. Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution, Cell, Volume 134 (2008) no. 2, pp. 341-352 | Article

[34] Duchemin, W.; Anselmetti, Y.; Patterson, M.; Ponty, Y.; B�rard, S.; Chauve, C.; Scornavacca, C.; Daubin, V.; Tannier, E. DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies, Genome Biology and Evolution, Volume 9 (2017) no. 5, pp. 1312-1319 | Article

[35] Dunning Jr., J. B. CRC Handbook of Avian Body Masses, CRC Press, (2007) | Article

[36] Duret, L.; Arndt, P. F. The Impact of Recombination on Nucleotide Substitutions in the Human Genome, PLoS Genetics, Volume 4 (2008) no. 5 | Article

[37] Duret, L.; Galtier, N. Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes, Annual Review of Genomics and Human Genetics, Volume 10 (2009) no. 1, pp. 285-311 | Article

[38] Dutheil, J.; Boussau, B. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs, BMC Evolutionary Biology, Volume 8 (2008) no. 1 | Article

[39] Dyke, G. J.; Cooper, J. H. A new psittaciform bird from the London Clay (Lower Eocene) of England, Palaeontology, Volume 43 (2008) no. 2, pp. 271-285 | Article

[40] Ellegren, H. The different levels of genetic diversity in sex chromosomes and autosomes, Trends in Genetics, Volume 25 (2009) no. 6, pp. 278-284 | Article

[41] Ellegren, H. Evolutionary stasis: the stable chromosomes of birds, Trends in Ecology & Evolution, Volume 25 (2010) no. 5, pp. 283-291 | Article

[42] Ellegren, H. The Evolutionary Genomics of Birds, Annual Review of Ecology, Evolution, and Systematics, Volume 44 (2013) no. 1, pp. 239-259 | Article

[43] Ellegren, H.; Smeds, L.; Burri, R.; Olason, P. I.; Backström, N.; Kawakami, T.; Künstner, A.; Mäkinen, H.; Nadachowska-Brzyska, K.; Qvarnström, A.; Uebbing, S.; Wolf, J. B. W. The genomic landscape of species divergence in Ficedula flycatchers, Nature, Volume 491 (2012) no. 7426, pp. 756-760 | Article

[44] Emms, D. M.; Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biology, Volume 16 (2015) no. 1 | Article

[45] Ericson, P. G.; Klopfstein, S.; Irestedt, M.; Nguyen, J. M.; Nylander, J. A. Dating the diversification of the major lineages of Passeriformes (Aves), BMC Evolutionary Biology, Volume 14 (2014) no. 1 | Article

[46] Eyre-Walker A., Recombination and mammalian genome evolution, Proceedings of the Royal Society of London. Series B: Biological Sciences, Volume 252 (1993) no. 1335, pp. 237-243 | Article

[47] Fraïsse, C.; Picard, M. A. L.; Vicoso, B. The deep conservation of the Lepidoptera Z chromosome suggests a non-canonical origin of the W, Nature Communications, Volume 8 (2017) no. 1 | Article

[48] Galtier, N.; Gouy, M. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis, Molecular Biology and Evolution, Volume 15 (1998) no. 7, pp. 871-879 | Article

[49] Genner, M. J.; Seehausen, O.; Lunt, D. H.; Joyce, D. A.; Shaw, P. W.; Carvalho, G. R.; Turner, G. F. Age of Cichlids: New Dates for Ancient Lake Fish Radiations, Molecular Biology and Evolution, Volume 24 (2007) no. 5, pp. 1269-1282 | Article

[50] Gill, F. B. Intra-Island Variation in the Mascarene White-Eye Zosterops borbonica, Ornithological Monographs (1973) no. 12 | Article

[51] Griffin, D.; Robertson, L.; Tempest, H.; Skinner, B. The evolution of the avian genome as revealed by comparative molecular cytogenetics, Cytogenetic and Genome Research, Volume 117 (2007) no. 1-4, pp. 64-77 | Article

[52] Gu, Z.; Gu, L.; Eils, R.; Schlesner, M.; Brors, B. Circlize implements and enhances circular visualization in R, Bioinformatics, Volume 30 (2014) no. 19, pp. 2811-2812 | Article

[53] Guéguen, L.; Gaillard, S.; Boussau, B.; Gouy, M.; Groussin, M.; Rochette, N. C.; Bigot, T.; Fournier, D.; Pouyet, F.; Cahais, V.; Bernard, A.; Scornavacca, C.; Nabholz, B.; Haudry, A.; Dachary, L.; Galtier, N.; Belkhir, K.; Dutheil, J. Y. Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution, Molecular Biology and Evolution, Volume 30 (2013) no. 8, pp. 1745-1750 | Article

[54] Haas, B. J. e. a. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucleic Acids Research, Volume 31 (2003) no. 19, pp. 5654-5666 | Article

[55] Haas, B. J.; Papanicolaou, A.; Yassour, M.; Grabherr, M.; Blood, P. D.; Bowden, J.; Couger, M. B.; Eccles, D.; Li, B.; Lieber, M.; MacManes, M. D.; Ott, M.; Orvis, J.; Pochet, N.; Strozzi, F.; Weeks, N.; Westerman, R.; William, T.; Dewey, C. N.; Henschel, R.; LeDuc, R. D.; Friedman, N.; Regev, A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nature Protocols, Volume 8 (2013) no. 8, pp. 1494-1512 | Article

[56] Haas, B. J.; Salzberg, S. L.; Zhu, W.; Pertea, M.; Allen, J. E.; Orvis, J.; White, O.; Buell, C. R.; Wortman, J. R. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments, Genome Biology, Volume 9 (2008) no. 1 | Article

[57] Haas BJ, ; Zeng Q, ; Pearson MD, ; Cuomo CA, ; Wortman JR, Approaches to Fungal Genome Annotation, Mycology, Volume 2 (2011), pp. 118-141 | Article

[58] Hahn, C.; Bachmann, L.; Chevreux, B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach, Nucleic Acids Research, Volume 41 (2013) no. 13 | Article

[59] Harmon, L. Phylogenetic Comparative Methods: Learning From Trees, Phylogenetic Comparative Methods: Learning from Trees. CreateSpace. EcoEvoRxiv, (2019) | Article

[60] Heads, M. Dating nodes on molecular phylogenies: a critique of molecular biogeography, Cladistics, Volume 21 (2005) no. 1, pp. 62-78 | Article

[61] Heads, M. Old Taxa on Young Islands: A Critique of the Use of Island Age to Date Island-Endemic Clades and Calibrate Phylogenies, Systematic Biology, Volume 60 (2011) no. 2, pp. 204-218 | Article

[62] Hill, W. G.; Robertson, A. The effect of linkage on limits to artificial selection, Genetical Research, Volume 8 (1966) no. 3, pp. 269-294 | Article

[63] Hughes, G. M.; Teeling, E. C. AGILE: an assembled genome mining pipeline, Bioinformatics, Volume 35 (2018) no. 7, pp. 1252-1254 | Article

[64] Hvilsom, C.; Qian, Y.; Bataillon, T.; Li, Y.; Mailund, T.; Salle, B.; Carlsen, F.; Li, R.; Zheng, H.; Jiang, T.; Jiang, H.; Jin, X.; Munch, K.; Hobolth, A.; Siegismund, H. R.; Wang, J.; Schierup, M. H. Extensive X-linked adaptive evolution in central chimpanzees, Proceedings of the National Academy of Sciences, Volume 109 (2012) no. 6, pp. 2054-2059 | Article

[65] International Chicken Genome Sequencing Consortium, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, Volume 432 (2004) no. 7018, pp. 695-716 | Article

[66] Jarvis, E. D.; Mirarab, S.; Aberer, A. J.; Li, B.; Houde, P.; Li, C.; Ho, S. Y. W.; Faircloth, B. C.; Nabholz, B.; Howard, J. T.; Suh, A.; Weber, C. C.; da Fonseca, R. R.; Li, J.; Zhang, F.; Li, H.; Zhou, L.; Narula, N.; Liu, L.; Ganapathy, G.; Boussau, B.; Bayzid, M. S.; Zavidovych, V.; Subramanian, S.; Gabaldón, T.; Capella-Gutiérrez, S.; Huerta-Cepas, J.; Rekepalli, B.; Munch, K.; Schierup, M.; Lindow, B.; Warren, W. C.; Ray, D.; Green, R. E.; Bruford, M. W.; Zhan, X.; Dixon, A.; Li, S.; Li, N.; Huang, Y.; Derryberry, E. P.; Bertelsen, M. F.; Sheldon, F. H.; Brumfield, R. T.; Mello, C. V.; Lovell, P. V.; Wirthlin, M.; Schneider, M. P. C.; Prosdocimi, F.; Samaniego, J. A.; Velazquez, A. M. V.; Alfaro-Núñez, A.; Campos, P. F.; Petersen, B.; Sicheritz-Ponten, T.; Pas, A.; Bailey, T.; Scofield, P.; Bunce, M.; Lambert, D. M.; Zhou, Q.; Perelman, P.; Driskell, A. C.; Shapiro, B.; Xiong, Z.; Zeng, Y.; Liu, S.; Li, Z.; Liu, B.; Wu, K.; Xiao, J.; Yinqi, X.; Zheng, Q.; Zhang, Y.; Yang, H.; Wang, J.; Smeds, L.; Rheindt, F. E.; Braun, M.; Fjeldsa, J.; Orlando, L.; Barker, F. K.; Jønsson, K. A.; Johnson, W.; Koepfli, K.-P.; O’Brien, S.; Haussler, D.; Ryder, O. A.; Rahbek, C.; Willerslev, E.; Graves, G. R.; Glenn, T. C.; McCormack, J.; Burt, D.; Ellegren, H.; Alström, P.; Edwards, S. V.; Stamatakis, A.; Mindell, D. P.; Cracraft, J.; Braun, E. L.; Warnow, T.; Jun, W.; Gilbert, M. T. P.; Zhang, G. Whole-genome analyses resolve early branches in the tree of life of modern birds, Science, Volume 346 (2014) no. 6215, pp. 1320-1331 | Article

[67] Jetz, W.; Thomas, G. H.; Joy, J. B.; Hartmann, K.; Mooers, A. O. The global diversity of birds in space and time, Nature, Volume 491 (2012) no. 7424, pp. 444-448 | Article

[68] Jurka, J.; Kapitonov, V.; Pavlicek, A.; Klonowski, P.; Kohany, O.; Walichiewicz, J. Repbase Update, a database of eukaryotic repetitive elements, Cytogenetic and Genome Research, Volume 110 (2005) no. 1-4, pp. 462-467 | Article

[69] Kampstra, P. Beanplot: A Boxplot Alternative for Visual Comparison of Distributions, Journal of Statistical Software, Volume 28 (2008) no. Code Snippet 1, pp. 1-9 | Article

[70] Kapusta, A.; Suh, A. Evolution of bird genomes-a transposon's-eye view, Annals of the New York Academy of Sciences, Volume 1389 (2017) no. 1, pp. 164-185 | Article

[71] Katoh, K. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, Volume 30 (2002) no. 14, pp. 3059-3066 | Article

[72] Kawakami, T.; Smeds, L.; Backström, N.; Husby, A.; Qvarnström, A.; Mugal, C. F.; Olason, P.; Ellegren, H. A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution, Molecular Ecology, Volume 23 (2014) no. 16, pp. 4035-4058 | Article

[73] Kim, D.; Langmead, B.; Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements, Nature Methods, Volume 12 (2015) no. 4, pp. 357-360 | Article

[74] Kitano, J.; Peichel, C. L. Turnover of sex chromosomes and speciation in fishes, Environmental Biology of Fishes, Volume 94 (2011) no. 3, pp. 549-558 | Article

[75] Kitano, J.; Ross, J. A.; Mori, S.; Kume, M.; Jones, F. C.; Chan, Y. F.; Absher, D. M.; Grimwood, J.; Schmutz, J.; Myers, R. M.; Kingsley, D. M.; Peichel, C. L. A role for a neo-sex chromosome in stickleback speciation, Nature, Volume 461 (2009) no. 7267, pp. 1079-1083 | Article

[76] Ksepka, D.; Clarke, J. Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves, Palaeontologia Electronica (2015), pp. 1-25 | Article

[77] Lagomarsino, L. P.; Condamine, F. L.; Antonelli, A.; Mulch, A.; Davis, C. C. The abiotic and biotic drivers of rapid diversification in A ndean bellflowers (Campanulaceae), New Phytologist, Volume 210 (2016) no. 4, pp. 1430-1442 | Article

[78] Lanfear, R.; Kokko, H.; Eyre-Walker, A. Population size and the rate of evolution, Trends in Ecology & Evolution, Volume 29 (2014) no. 1, pp. 33-41 | Article

[79] Lartillot, N.; Lepage, T.; Blanquart, S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, Bioinformatics, Volume 25 (2009) no. 17, pp. 2286-2288 | Article

[80] Lee, M. S. Y.; Cau, A.; Naish, D.; Dyke, G. J. Morphological Clocks in Paleontology, and a Mid-Cretaceous Origin of Crown Aves, Systematic Biology, Volume 63 (2014) no. 3, pp. 442-449 | Article

[81] Leggett, R. M.; Clavijo, B. J.; Clissold, L.; Clark, M. D.; Caccamo, M. NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries, Bioinformatics, Volume 30 (2014) no. 4, pp. 566-568 | Article

[82] Lemon J, Plotrix: A package in the red light district of R, R-News, Volume 6 (2006), pp. 8-12

[83] Li H, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv, https://arxiv.org/abs/1303.3997 (2013)

[84] Lundberg, M.; Liedvogel, M.; Larson, K.; Sigeman, H.; Grahn, M.; Wright, A.; Åkesson, S.; Bensch, S. Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks, Evolution Letters, Volume 1 (2017) no. 3, pp. 155-168 | Article

[85] Luo, R.; Liu, B.; Xie, Y.; Li, Z.; Huang, W.; Yuan, J.; He, G.; Chen, Y.; Pan, Q.; Liu, Y.; Tang, J.; Wu, G.; Zhang, H.; Shi, Y.; Liu, Y.; Yu, C.; Wang, B.; Lu, Y.; Han, C.; Cheung, D. W.; Yiu, S.-M.; Peng, S.; Xiaoqian, Z.; Liu, G.; Liao, X.; Li, Y.; Yang, H.; Wang, J.; Lam, T.-W.; Wang, J. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, GigaScience, Volume 1 (2012) no. 1 | Article

[86] Magallón, S.; Sanderson, M. J. Absolute diversification rates in angiosperm clades, Evolution, Volume 55 (2001) no. 9 | Article

[87] Mank, J. E.; Axelsson, E.; Ellegren, H. Fast-X on the Z: Rapid evolution of sex-linked genes in birds, Genome Research, Volume 17 (2007) no. 5, pp. 618-624 | Article

[88] Mank, J. E.; Nam, K.; Ellegren, H. Faster-Z Evolution Is Predominantly Due to Genetic Drift, Molecular Biology and Evolution, Volume 27 (2010) no. 3, pp. 661-670 | Article

[89] Marais, G. A.; Nicolas, M.; Bergero, R.; Chambrier, P.; Kejnovsky, E.; Monéger, F.; Hobza, R.; Widmer, A.; Charlesworth, D. Evidence for Degeneration of the Y Chromosome in the Dioecious Plant Silene latifolia, Current Biology, Volume 18 (2008) no. 7, pp. 545-549 | Article

[90] Mayr, G.; Manegold, A. A Small Suboscine-Like Passeriform Bird from the Early Oligocene of France, The Condor, Volume 108 (2006) no. 3, pp. 717-720 | Article

[91] Mayr, G. The age of the crown group of passerine birds and its evolutionary significance – molecular calibrations versus the fossil record, Systematics and Biodiversity, Volume 11 (2013) no. 1, pp. 7-13 | Article

[92] Melo, M.; Warren, B. H.; Jones, P. J. Rapid parallel evolution of aberrant traits in the diversification of the Gulf of Guinea white-eyes (Aves, Zosteropidae), Molecular Ecology, Volume 20 (2011) no. 23, pp. 4953-4967 | Article

[93] Milá, B.; Warren, B. H.; Heeb, P.; Thébaud, C. The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus), BMC Evolutionary Biology, Volume 10 (2010) no. 1 | Article

[94] Moyle, R. G.; Filardi, C. E.; Smith, C. E.; Diamond, J. Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”, Proceedings of the National Academy of Sciences, Volume 106 (2009) no. 6, pp. 1863-1868 | Article

[95] Murphy, W. J.; Sun, S.; Chen, Z.-Q.; Pecon-Slattery, J.; O'Brien, S. J. Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping, Genome Research, Volume 9 (1999) no. 12, pp. 1223-1230 | Article

[96] Nabholz, B.; Kunstner, A.; Wang, R.; Jarvis, E. D.; Ellegren, H. Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics, Molecular Biology and Evolution, Volume 28 (2011) no. 8, pp. 2197-2210 | Article

[97] Nabholz, B.; Lanfear, R.; Fuchs, J. Body mass-corrected molecular rate for bird mitochondrial DNA, Molecular Ecology, Volume 25 (2016) no. 18, pp. 4438-4449 | Article

[98] Nam, K.; Munch, K.; Hobolth, A.; Dutheil, J. Y.; Veeramah, K. R.; Woerner, A. E.; Hammer, M. F.; Mailund, T.; Schierup, M. H. Extreme selective sweeps independently targeted the X chromosomes of the great apes, Proceedings of the National Academy of Sciences, Volume 112 (2015) no. 20, pp. 6413-6418 | Article

[99] Nanda, I.; Karl, E.; Volobouev, V.; Griffin, D.; Schartl, M.; Schmid, M. Extensive gross genomic rearrangements between chicken and Old World vultures (Falconiformes: Accipitridae), Cytogenetic and Genome Research, Volume 112 (2006) no. 3-4, pp. 286-295 | Article

[100] Nanda, I.; Schlegelmilch, K.; Haaf, T.; Schartl, M.; Schmid, M. Synteny conservation of the Z chromosome in 14 avian species (11 families) supports a role for Z dosage in avian sex determination, Cytogenetic and Genome Research, Volume 122 (2008) no. 2, pp. 150-156 | Article

[101] Nguyen, L.-P.; Galtier, N.; Nabholz, B. Gene expression, chromosome heterogeneity and the fast-X effect in mammals, Biology Letters, Volume 11 (2015) no. 2 | Article

[102] Nguyen, L.-T.; Schmidt, H. A.; von Haeseler, A.; Minh, B. Q. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies, Molecular Biology and Evolution, Volume 32 (2015) no. 1, pp. 268-274 | Article

[103] Oatley, G.; De Swardt, D. H.; Nuttall, R. J.; Crowe, T. M.; Bowie, R. C. K. Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South Africa, Biological Journal of the Linnean Society, Volume 121 (2017) no. 3, pp. 670-684 | Article

[104] Oatley, G.; Voelker, G.; Crowe, T. M.; Bowie, R. C. A multi-locus phylogeny reveals a complex pattern of diversification related to climate and habitat heterogeneity in southern African white-eyes, Molecular Phylogenetics and Evolution, Volume 64 (2012) no. 3, pp. 633-644 | Article

[105] O’Connor, R. E.; Romanov, M. N.; Kiazim, L. G.; Barrett, P. M.; Farré, M.; Damas, J.; Ferguson-Smith, M.; Valenzuela, N.; Larkin, D. M.; Griffin, D. K. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs, Nature Communications, Volume 9 (2018) no. 1 | Article

[106] Ohta, T. The Nearly Neutral Theory of Molecular Evolution, Annual Review of Ecology and Systematics, Volume 23 (1992) no. 1, pp. 263-286 | Article

[107] de Oliveira, E. H. C.; Habermann, F. A.; Lacerda, O.; Sbalqueiro, I. J.; Wienberg, J.; Müller, S. 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, Volume 114 (2005) no. 5, pp. 338-343 | Article

[108] Pala, I.; Naurin, S.; Stervander, M.; Hasselquist, D.; Bensch, S.; Hansson, B. Evidence of a neo-sex chromosome in birds, Heredity, Volume 108 (2012) no. 3, pp. 264-272 | Article

[109] Pala, I.; Hasselquist, D.; Bensch, S.; Hansson, B. Patterns of Molecular Evolution of an Avian Neo-sex Chromosome, Molecular Biology and Evolution, Volume 29 (2012) no. 12, pp. 3741-3754 | Article

[110] Papadopulos, A. S. T.; Chester, M.; Ridout, K.; Filatov, D. A. Rapid Y degeneration and dosage compensation in plant sex chromosomes, Proceedings of the National Academy of Sciences, Volume 112 (2015) no. 42, pp. 13021-13026 | Article

[111] Paradis, E.; Claude, J.; Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, Volume 20 (2004) no. 2, pp. 289-290 | Article

[112] Pedersen, B. S.; Quinlan, A. R. Mosdepth: quick coverage calculation for genomes and exomes, Bioinformatics, Volume 34 (2018) no. 5, pp. 867-868 | Article

[113] Peona, V.; Weissensteiner, M. H.; Suh, A. How complete are “complete” genome assemblies?-An avian perspective, Molecular Ecology Resources, Volume 18 (2018) no. 6, pp. 1188-1195 | Article

[114] Pertea, M.; Pertea, G. M.; Antonescu, C. M.; Chang, T.-C.; Mendell, J. T.; Salzberg, S. L. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nature Biotechnology, Volume 33 (2015) no. 3, pp. 290-295 | Article

[115] Pessia, E.; Popa, A.; Mousset, S.; Rezvoy, C.; Duret, L.; Marais, G. A. B. Evidence for Widespread GC-biased Gene Conversion in Eukaryotes, Genome Biology and Evolution, Volume 4 (2012) no. 7, pp. 675-682 | Article

[116] Philippe, H.; Vienne, D. M. d.; Ranwez, V.; Roure, B.; Baurain, D.; Delsuc, F. Pitfalls in supermatrix phylogenomics, European Journal of Taxonomy, Volume 283 (2017), pp. 1-25 | Article

[117] Poelstra, J. W.; Vijay, N.; Bossu, C. M.; Lantz, H.; Ryll, B.; Müller, I.; Baglione, V.; Unneberg, P.; Wikelski, M.; Grabherr, M. G.; Wolf, J. B. W. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows, Science, Volume 344 (2014) no. 6190, pp. 1410-1414 | Article

[118] Pool, J. E.; Nielsen, R. Population size changes reshape genomic patterns of diversity, Evolution, Volume 61 (2007) no. 12, pp. 3001-3006 | Article

[119] Prum, R. O.; Berv, J. S.; Dornburg, A.; Field, D. J.; Townsend, J. P.; Lemmon, E. M.; Lemmon, A. R. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing, Nature, Volume 526 (2015) no. 7574, pp. 569-573 | Article

[120] R core team, R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing, (2018)

[121] Rannala, B.; Yang, Z. Inferring Speciation Times under an Episodic Molecular Clock, Systematic Biology, Volume 56 (2007) no. 3, pp. 453-466 | Article

[122] Ranwez, V.; Douzery, E. J. P.; Cambon, C.; Chantret, N.; Delsuc, F. MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons, Molecular Biology and Evolution, Volume 35 (2018) no. 10, pp. 2582-2584 | Article

[123] Raudsepp, T.; Santani, A.; Wallner, B.; Kata, S. R.; Ren, C.; Zhang, H.-B.; Womack, J. E.; Skow, L. C.; Chowdhary, B. P. A detailed physical map of the horse Y chromosome, Proceedings of the National Academy of Sciences, Volume 101 (2004) no. 25, pp. 9321-9326 | Article

[124] Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things), Methods in Ecology and Evolution, Volume 3 (2012) no. 2, pp. 217-223 | Article

[125] Rousselle, M.; Faivre, N.; Ballenghien, M.; Galtier, N.; Nabholz, B. Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies, Genome Biology and Evolution, Volume 8 (2016) no. 10, pp. 3108-3119 | Article

[126] Roux, C.; Fraïsse, C.; Romiguier, J.; Anciaux, Y.; Galtier, N.; Bierne, N. Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence, PLOS Biology, Volume 14 (2016) no. 12 | Article

[127] Salmela, L.; Rivals, E. LoRDEC: accurate and efficient long read error correction, Bioinformatics, Volume 30 (2014) no. 24, pp. 3506-3514 | Article

[128] Schwartz, S.; Kent, W. J.; Smit, A.; Zhang, Z.; Baertsch, R.; Hardison, R. C.; Haussler, D.; Miller, W. Human–Mouse Alignments with BLASTZ, Genome Research, Volume 13 (2003) no. 1, pp. 103-107 | Article

[129] She, R.; Chu, J. S.-C.; Uyar, B.; Wang, J.; Wang, K.; Chen, N. genBlastG: using BLAST searches to build homologous gene models, Bioinformatics, Volume 27 (2011) no. 15, pp. 2141-2143 | Article

[130] Sigeman, H.; Ponnikas, S.; Videvall, E.; Zhang, H.; Chauhan, P.; Naurin, S.; Hansson, B. Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat, Genes, Volume 9 (2018) no. 8 | Article

[131] Sigeman H, ; Ponnikas S, ; Chauhan P, ; Dierickx E, ; Brooke ML, ; Hansson B, Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes, Proceedings of the Royal Society B., Volume 286 (2019) | Article

[132] Smeds, L.; Warmuth, V.; Bolivar, P.; Uebbing, S.; Burri, R.; Suh, A.; Nater, A.; Bureš, S.; Garamszegi, L. Z.; Hogner, S.; Moreno, J.; Qvarnström, A.; Ružić, M.; Sæther, S.-A.; Sætre, G.-P.; Török, J.; Ellegren, H. Evolutionary analysis of the female-specific avian W chromosome, Nature Communications, Volume 6 (2015) no. 1 | Article

[133] Suh A, ; Smeds L, ; Ellegren H. , Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes, Molecular Ecology, Volume 27 (2018), pp. 99-111 | Article

[134] Smit A, ; Hubley R, RepeatModeler Open-1.0, (2008)

[135] Smit A, ; Hubley R, ; Green P, RepeatMasker Open-4.0, (2013)

[136] Stanke M, ; Waack S, Gene prediction with a hidden markov model and a new intron submodel, Bioinformatics, Volume 19 (2003), pp. 215-225 | Article

[137] Sun, S.; Heitman, J. Should Y stay or should Y go: The evolution of non-recombining sex chromosomes, BioEssays, Volume 34 (2012) no. 11, pp. 938-942 | Article

[138] Tajima F, Evolutionary relationship of DNA sequences in finite populations, Genetics, Volume 105 (1983), pp. 437-460 | Article

[139] Tilak, M.-K.; Botero-Castro, F.; Galtier, N.; Nabholz, B. Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA, Genome Biology and Evolution, Volume 10 (2018) no. 2, pp. 616-622 | Article

[140] Tomaszkiewicz, M.; Medvedev, P.; Makova, K. D. Y and W Chromosome Assemblies: Approaches and Discoveries, Trends in Genetics, Volume 33 (2017) no. 4, pp. 266-282 | Article

[141] Trapnell, C.; Williams, B. A.; Pertea, G.; Mortazavi, A.; Kwan, G.; van Baren, M. J.; Salzberg, S. L.; Wold, B. J.; Pachter, L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology, Volume 28 (2010) no. 5, pp. 511-515 | Article

[142] Vicoso, B.; Charlesworth, B. Evolution on the X chromosome: unusual patterns and processes, Nature Reviews Genetics, Volume 7 (2006) no. 8, pp. 645-653 | Article

[143] Völker, M.; Backström, N.; Skinner, B. M.; Langley, E. J.; Bunzey, S. K.; Ellegren, H.; Griffin, D. K. Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution, Genome Research, Volume 20 (2010) no. 4, pp. 503-511 | Article

[144] Warren, W. C.; Clayton, D. F.; Ellegren, H.; Arnold, A. P.; Hillier, L. W.; Künstner, A.; Searle, S.; White, S.; Vilella, A. J.; Fairley, S.; Heger, A.; Kong, L.; Ponting, C. P.; Jarvis, E. D.; Mello, C. V.; Minx, P.; Lovell, P.; Velho, T. A. F.; Ferris, M.; Balakrishnan, C. N.; Sinha, S.; Blatti, C.; London, S. E.; Li, Y.; Lin, Y.-C.; George, J.; Sweedler, J.; Southey, B.; Gunaratne, P.; Watson, M.; Nam, K.; Backström, N.; Smeds, L.; Nabholz, B.; Itoh, Y.; Whitney, O.; Pfenning, A. R.; Howard, J.; Völker, M.; Skinner, B. M.; Griffin, D. K.; Ye, L.; McLaren, W. M.; Flicek, P.; Quesada, V.; Velasco, G.; Lopez-Otin, C.; Puente, X. S.; Olender, T.; Lancet, D.; Smit, A. F. A.; Hubley, R.; Konkel, M. K.; Walker, J. A.; Batzer, M. A.; Gu, W.; Pollock, D. D.; Chen, L.; Cheng, Z.; Eichler, E. E.; Stapley, J.; Slate, J.; Ekblom, R.; Birkhead, T.; Burke, T.; Burt, D.; Scharff, C.; Adam, I.; Richard, H.; Sultan, M.; Soldatov, A.; Lehrach, H.; Edwards, S. V.; Yang, S.-P.; Li, X.; Graves, T.; Fulton, L.; Nelson, J.; Chinwalla, A.; Hou, S.; Mardis, E. R.; Wilson, R. K. The genome of a songbird, Nature, Volume 464 (2010) no. 7289, pp. 757-762 | Article

[145] Warren WC et al., A New Chicken Genome Assembly Provides Insight into Avian Genome Structure, G3: Genes|Genomes|Genetics, Volume 7 (2016), pp. 109-117 | Article

[146] Waterhouse, R. M.; Seppey, M.; Simão, F. A.; Manni, M.; Ioannidis, P.; Klioutchnikov, G.; Kriventseva, E. V.; Zdobnov, E. M. BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics, Molecular Biology and Evolution, Volume 35 (2017) no. 3, pp. 543-548 | Article

[147] Weber, C. C.; Boussau, B.; Romiguier, J.; Jarvis, E. D.; Ellegren, H. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition, Genome Biology, Volume 15 (2014) no. 12 | Article

[148] Weingartner LA, ; Delph LF , Neo‐sex chromosome inheritance across species in Silene hybrids?, Journal of Evolutionary Biology, Volume 27 (2014), pp. 1491-1499 | Article

[149] Weissensteiner, M. H.; Pang, A. W.; Bunikis, I.; Höijer, I.; Vinnere-Petterson, O.; Suh, A.; Wolf, J. B. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications, Genome Research, Volume 27 (2017) no. 5, pp. 697-708 | Article

[150] Wickham, H. ggplot2, Use R!, Springer International Publishing, Cham, 2016 | Article

[151] Wilke C, cowplot: Streamlined Plot Theme and Plot Annotations for ‘ggplot2’ https://doi.org/10.5281/zenodo.2533860, (2016)

[152] Wilson Sayres, M. A. Genetic Diversity on the Sex Chromosomes, Genome Biology and Evolution, Volume 10 (2018) no. 4, pp. 1064-1078 | Article

[153] Wolf, J. B. W.; Künstner, A.; Nam, K.; Jakobsson, M.; Ellegren, H. Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection, Genome Biology and Evolution, Volume 1 (2009), pp. 308-319 | Article

[154] Wright, A. E.; Harrison, P. W.; Zimmer, F.; Montgomery, S. H.; Pointer, M. A.; Mank, J. E. Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution, Molecular Ecology, Volume 24 (2015) no. 6, pp. 1218-1235 | Article

[155] Yang Z, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, Volume 24 (2007), pp. 1586-1591 | Article

[156] Yang, Z.; Rannala, B. Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds, Molecular Biology and Evolution, Volume 23 (2005) no. 1, pp. 212-226 | Article

[157] Yoshida, K.; Makino, T.; Yamaguchi, K.; Shigenobu, S.; Hasebe, M.; Kawata, M.; Kume, M.; Mori, S.; Peichel, C. L.; Toyoda, A.; Fujiyama, A.; Kitano, J. Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species, PLoS Genetics, Volume 10 (2014) no. 3 | Article

[158] Zhang, G.; Li, C.; Li, Q.; Li, B.; Larkin, D. M.; Lee, C.; Storz, J. F.; Antunes, A.; Greenwold, M. J.; Meredith, R. W.; Ödeen, A.; Cui, J.; Zhou, Q.; Xu, L.; Pan, H.; Wang, Z.; Jin, L.; Zhang, P.; Hu, H.; Yang, W.; Hu, J.; Xiao, J.; Yang, Z.; Liu, Y.; Xie, Q.; Yu, H.; Lian, J.; Wen, P.; Zhang, F.; Li, H.; Zeng, Y.; Xiong, Z.; Liu, S.; Zhou, L.; Huang, Z.; An, N.; Wang, J.; Zheng, Q.; Xiong, Y.; Wang, G.; Wang, B.; Wang, J.; Fan, Y.; da Fonseca, R. R.; Alfaro-Núñez, A.; Schubert, M.; Orlando, L.; Mourier, T.; Howard, J. T.; Ganapathy, G.; Pfenning, A.; Whitney, O.; Rivas, M. V.; Hara, E.; Smith, J.; Farré, M.; Narayan, J.; Slavov, G.; Romanov, M. N.; Borges, R.; Machado, J. P.; Khan, I.; Springer, M. S.; Gatesy, J.; Hoffmann, F. G.; Opazo, J. C.; Håstad, O.; Sawyer, R. H.; Kim, H.; Kim, K.-W.; Kim, H. J.; Cho, S.; Li, N.; Huang, Y.; Bruford, M. W.; Zhan, X.; Dixon, A.; Bertelsen, M. F.; Derryberry, E.; Warren, W.; Wilson, R. K.; Li, S.; Ray, D. A.; Green, R. E.; O’Brien, S. J.; Griffin, D.; Johnson, W. E.; Haussler, D.; Ryder, O. A.; Willerslev, E.; Graves, G. R.; Alström, P.; Fjeldså, J.; Mindell, D. P.; Edwards, S. V.; Braun, E. L.; Rahbek, C.; Burt, D. W.; Houde, P.; Zhang, Y.; Yang, H.; Wang, J.; Jarvis, E. D.; Gilbert, M. T. P.; Wang, J.; Ye, C.; Liang, S.; Yan, Z.; Zepeda, M. L.; Campos, P. F.; Velazquez, A. M. V.; Samaniego, J. A.; Avila-Arcos, M.; Martin, M. D.; Barnett, R.; Ribeiro, A. M.; Mello, C. V.; Lovell, P. V.; Almeida, D.; Maldonado, E.; Pereira, J.; Sunagar, K.; Philip, S.; Dominguez-Bello, M. G.; Bunce, M.; Lambert, D.; Brumfield, R. T.; Sheldon, F. H.; Holmes, E. C.; Gardner, P. P.; Steeves, T. E.; Stadler, P. F.; Burge, S. W.; Lyons, E.; Smith, J.; McCarthy, F.; Pitel, F.; Rhoads, D.; Froman, D. P. Comparative genomics reveals insights into avian genome evolution and adaptation, Science, Volume 346 (2014) no. 6215, pp. 1311-1320 | Article

[159] Zhang G, ; Parker P, ; Li B, ; Li H, ; Wang J, The genome of Darwin’s Finch (Geospiza fortis), GigaScience (2012) | Article

[160] Zhou, Q.; Bachtrog, D. Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila, Science, Volume 337 (2012) no. 6092, pp. 341-345 | Article

[161] Zimin, A. V.; Puiu, D.; Luo, M.-C.; Zhu, T.; Koren, S.; Marçais, G.; Yorke, J. A.; Dvořák, J.; Salzberg, S. L. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm, Genome Research, Volume 27 (2017) no. 5, pp. 787-792 | Article

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