Bachtrog, D., 2013. Y-chromosome evolution:emerging insights into processes of Y-chromosome degeneration. Nat. Rev. Genet. 14, 113-124
|
Bai, Y., Casola, C., Feschotte, C., Betran, E., 2007. Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome. Biol. 8, R11
|
Baker, A.J., Haddrath, O., McPherson, J.D., Cloutier, A., 2014. Genomic Support for a Moa-Tinamou Clade and Adaptive Morphological Convergence in Flightless Ratites. Mol. Biol. Evol. 31, 1686-1696
|
Bao, W., Kojima, K.K., Kohany, O., 2015. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile. Dna-uk. 6, 11
|
Benson, G., 1999. Tandem repeats finder:a program to analyze DNA sequences. Nucleic. Acids. Res. 27, 573-580
|
Bernt, M., Donath, A., Juhling, F., Externbrink, F., Florentz, C., Fritzsch, G., Putz, J., Middendorf, M., Stadler, P.F., 2013. MITOS:Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313-319
|
Berv, J.S., Field, D.J., 2018. Genomic Signature of an Avian Lilliput Effect across the K-Pg Extinction. Systematic. Biol. 67, 1-13
|
Betran, E., Thornton, K., Long, M., 2002. Retroposed New Genes Out of the X in Drosophila. Genome. Res. 12, 1854-1859
|
Birney, E., Clamp, M., Durbin, R., 2004. GeneWise and Genomewise. Genome. Res. 14, 988-995
|
Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., et al., 2004. Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner. Genome. Res. 14, 708-715
|
Braun, E.L., Cracraft, J., Houde, P., 2019. Avian Genomics in Ecology and Evolution 151-210
|
Bromham, L., 2011. The genome as a life-history character:why rate of molecular evolution varies between mammal species. Philosophical. Transactions. Royal. Soc. Lond. Ser. B. Biological. Sci. 366, 2503-2513
|
Charlesworth, B., Charlesworth, D., 2000. The degeneration of Y chromosomes. Philosophical. Transactions. Royal. Soc. Lond. Ser. B. Biological. Sci. 355, 1563-1572
|
Cloutier, A., Sackton, T.B., Grayson, P., Clamp, M., Baker, A.J., Edwards, S.V., 2019. Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone. Systematic. Biol. 68, 937-955
|
Cockburn, A., 2006. Prevalence of different modes of parental care in birds. Proc. Royal. Soc. B. Biological. Sci. 273, 1375-1383
|
Coddington, C., Cockburn, A., 1995. The Mating System of Free-Living Emus. Aust. J. Zool. 43, 365
|
Cortez, D., Marin, R., Toledo-Flores, D., Froidevaux, L., Liechti, A., Waters, P.D., Grutzner, F., Kaessmann, H., 2014. Origins and functional evolution of Y chromosomes across mammals. Nature. 508, 488-493
|
Cracraft, J., 1974. Phylogeny and evolution of the ratite birds. Ibis. 116, 494-521
|
DePristo, M.A., Banks, E., Poplin, R., Garimella, K.V., Maguire, J.R., Hartl, C., Philippakis, A.A., Angel, G. del, Rivas, M.A., Hanna, M., et al., 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498
|
Duc, D.L., Renaud, G., Krishnan, A., Almen, M.S., Huynen, L., Prohaska, S.J., Ongyerth, M., Bitarello, B.D., Schioth, H.B., Hofreiter, M., et al., 2015. Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome. Biol. 16, 147
|
Edgar, R.C., 2004. MUSCLE:multiple sequence alignment with high accuracy and high throughput. Nucleic. Acids. Res. 32, 1792-1797
|
Emerson, J.J., Kaessmann, H., Betran, E., Long, M., 2004. Extensive Gene Traffic on the Mammalian X Chromosome. Science. 303, 537-540
|
Graves, J.A.M., 2006. Sex Chromosome Specialization and Degeneration in Mammals. Cell. 124, 901-914
|
Grealy, A., Phillips, M., Miller, G., Gilbert, M.T.P., Rouillard, J.-M., Lambert, D., Bunce, M., Haile, J., 2017. Eggshell palaeogenomics:Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Mol. Phylogenet. Evol. 109, 151-163
|
Guioli, S., Lovell-Badge, R., Turner, J.M.A., 2012. Error-Prone ZW Pairing and No Evidence for Meiotic Sex Chromosome Inactivation in the Chicken Germ Line. Plos. Genet. 8, e1002560
|
Handford, P., Mares, M.A., 1985. The mating systems of ratites and tinamous:an evolutionary perspective. Biol. J. Linn. Soc. 25, 77-104
|
Harshman, J., Braun, E.L., Braun, M.J., Huddleston, C.J., Bowie, R.C.K., Chojnowski, J.L., Hackett, S.J., Han, K.-L., Kimball, R.T., Marks, B.D., et al., 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proc. National. Acad. Sci. U. S. A. 105, 13462-13467
|
Hubisz, M.J., Pollard, K.S., Siepel, A., 2011. PHAST and RPHAST:phylogenetic analysis with space/time models. Brief. Bioinform. 12, 41-51
|
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., et al., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 346, 1320-1331
|
Kapusta, A., Suh, A., Feschotte, C., 2017. Dynamics of genome size evolution in birds and mammals. P. Natl. Acad. Sci. U. S. A. 114, E1460-E1469
|
Katoh, K., Standley, D.M., 2013. MAFFT Multiple Sequence Alignment Software Version 7:Improvements in Performance and Usability. Mol. Biol. Evol. 30, 772-780
|
Kim, D., Langmead, B., Salzberg, S.L., 2015. HISAT:a fast spliced aligner with low memory requirements. Nat. Methods. 12, 357-360
|
Kozlov, A.M., Aberer, A.J., Stamatakis, A., 2015. ExaML version 3:a tool for phylogenomic analyses on supercomputers. Bioinform. Oxf. Engl. 31, 2577-2579
|
Krasovec, M., Chester, M., Ridout, K., Filatov, D.A., 2018. The Mutation Rate and the Age of the Sex Chromosomes in Silene latifolia. Curr. Biology. 28, 1832-1838.e4
|
Lahn, B.T., Page, D.C., 1999. Four Evolutionary Strata on the Human X Chromosome. Science. 286, 964-967
|
Li, H., Coghlan, A., Ruan, J., Coin, L.J., Heriche, J.-K., Osmotherly, L., Li, R., Liu, T., Zhang, Z., Bolund, L., et al., 2006. TreeFam:a curated database of phylogenetic trees of animal gene families. Nucleic. Acids. Res. 34, D572-D580
|
Li, H., Durbin, R., 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25, 1754-1760
|
Li, W.-H., Yi, S., Makova, K., 2002. Male-driven evolution. Curr. Opin. Genet. Dev. 12, 650-656
|
Lifschytz, E., Lindsley, D.L., 1972. The Role of X-Chromosome Inactivation during Spermatogenesis. Proc. National. Acad. Sci. 69, 182-186
|
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Yunjie, et al., 2012. SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler. Gigascience. 1, 18
|
Mank, J.E., Ellegren, H., 2007. Parallel divergence and degradation of the avian W sex chromosome. Trends. Ecol. Evol. 22, 389-391
|
McKee, B.D., Handel, M.A., 1993. Sex chromosomes, recombination, and chromatin conformation. Chromosoma. 102, 71-80
|
McNab, B.K., 1996. Metabolism and Temperature Regulation of Kiwis (Apterygidae). Auk. 113, 687-692
|
Meisel, R.P., Han, M.V., Hahn, M.W., 2009. A Complex Suite of Forces Drives Gene Traffic from Drosophila X Chromosomes. Genome. Biol. Evol. 1, 176-188
|
Meng, G., Li, Y., Yang, C., Liu, S., 2019. MitoZ:a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic. Acids. Res. 47, gkz173-
|
Mitchell, K.J., Llamas, B., Soubrier, J., Rawlence, N.J., Worthy, T.H., Wood, J., Lee, M.S.Y., Cooper, A., 2014. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution. Science. 344, 898-900
|
Miyata, T., Hayashida, H., Kuma, K., Mitsuyasu, K., Yasunaga, T., 1987. Male-driven Molecular Evolution:A Model and Nucleotide Sequence Analysis. Cold. Spring. Harb. Sym. 52, 863-867
|
Nishida-Umehara, C., Tsuda, Y., Ishijima, J., Ando, J., Fujiwara, A., Matsuda, Y., Griffin, D.K., 2007. The molecular basis of chromosome orthologies and sex chromosomal differentiation in palaeognathous birds. Chromosome. Res. 15, 721-734
|
O'Connor, R.E., Farre, M., Joseph, S., Damas, J., Kiazim, L., Jennings, R., Bennett, S., Slack, E.A., Allanson, E., Larkin, D.M., et al., 2018. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome. Biol. 19, 171
|
Paradis, E., Claude, J., Strimmer, K., 2004. APE:Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 20, 289-290
|
Parker, J., Tsagkogeorga, G., Cotton, J.A., Liu, Y., Provero, P., Stupka, E., Rossiter, S.J., 2013. Genome-wide signatures of convergent evolution in echolocating mammals. Nature. 502, 228-231
|
Pigozzi, M.I., 2011. Diverse stages of sex-chromosome differentiation in tinamid birds:evidence from crossover analysis in Eudromia elegans and Crypturellus tataupa. Genetica. 139, 771-777
|
Potrzebowski, L., Vinckenbosch, N., Marques, A.C., Chalmel, F., Jegou, B., Kaessmann, H., 2008. Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes. Plos. Biol. 6, e80
|
Prum, R.O., Berv, J.S., Dornburg, A., Field, D.J., Townsend, J.P., Lemmon, E.M., Lemmon, A.R., 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature. 526, 569-573
|
Remes, V., Freckleton, R.P., Tokolyi, J., Liker, A., Szekely, T., 2015. The evolution of parental cooperation in birds. P. Natl. Acad. Sci. U. S. A. 112, 13603-13608
|
Reynolds, J.D., Szekely, T., 1997. The evolution of parental care in shorebirds:life histories, ecology, and sexual selection. Behav. Ecol. 8, 126-134
|
Robinson, M.D., Oshlack, A., 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome. Biol. 11, R25
|
Ronquist, F., Huelsenbeck, J.P., 2003. MrBayes 3:Bayesian phylogenetic inference under mixed models. Bioinformatics. 19, 1572-1574
|
Sackton, T.B., Grayson, P., Cloutier, A., Hu, Z., Liu, J.S., Wheeler, N.E., Gardner, P.P., Clarke, J.A., Baker, A.J., Clamp, M., et al., 2019. Convergent regulatory evolution and loss of flight in paleognathous birds. Science. 364, 74-78
|
Stamatakis, A., 2014. RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinform. Oxf. Engl. 30, 1312-1313
|
Stanke, M., Steinkamp, R., Waack, S., Morgenstern, B., 2004. AUGUSTUS:a web server for gene finding in eukaryotes. Nucleic. Acids. Res. 32, W309-W312
|
Sturgill, D., Zhang, Y., Parisi, M., Oliver, B., 2007. Demasculinization of X chromosomes in the Drosophila genus. Nature. 450, 238-241
|
Szekely, T., 2014. Sexual Conflict between Parents:Offspring Desertion and Asymmetrical Parental Care. Csh. Perspect. Biol. 6, a017665-a017665
|
Takagi, N., Itoh, M., Sasaki, M., 1972. Chromosome studies in four species of Ratitae (Aves). Chromosoma. 36, 281-291
|
Tollis, M., Robbins, J., Webb, A.E., Kuderna, L.F.K., Caulin, A.F., Garcia, J.D., Berube, M., Pourmand, N., Marques-Bonet, T., O'Connell, et al., 2019. Return to the Sea, Get Huge, Beat Cancer:An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). Mol. Biol. Evol. 36, 1746-1763
|
Toups, M.A., Pease, J.B., Hahn, M.W., 2011. No Excess Gene Movement Is Detected off the Avian or Lepidopteran Z Chromosome. Genome. Biol. Evol. 3, 1381-1390
|
Traut, W., Schubert, V., Dalikova, M., Marec, F., Sahara, K., 2019. Activity and inactivity of moth sex chromosomes in somatic and meiotic cells. Chromosoma. 128, 533-545
|
Tullberg, B.S., Ah-King, M., Temrin, H., 2002. Phylogenetic reconstruction of parental-care systems in the ancestors of birds. Philosophical. Transactions. Royal. Soc. Lond. Ser. B. Biological. Sci. 357, 251-257
|
Turner, J.M.A., 2007. Meiotic sex chromosome inactivation. Development. 134, 1823-1831
|
Varricchio, D.J., Moore, J.R., Erickson, G.M., Norell, M.A., Jackson, F.D., Borkowski, J.J., 2008. Avian paternal care had dinosaur origin. Sci. New. York. N. Y. 322, 1826-1828
|
Vibranovski, M.D., Lopes, H.F., Karr, T.L., Long, M., 2009a. Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed Genes. PLoS. Genet. 5, e1000731
|
Vibranovski, M.D., Zhang, Y., Long, M., 2009b. General gene movement off the X chromosome in the Drosophila genus. Genome. Res. 19, 897-903
|
Vicoso, B., Kaiser, V.B., Bachtrog, D., 2013. Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. P. Natl. Acad. Sci. U. S. A. 110, 6453-6458
|
Wang, J., Long, M., Vibranovski, M.D., 2012. Retrogenes Moved Out of the Z Chromosome in the Silkworm. J. Mol. Evol. 74, 113-126
|
Wang, Z.-J., Chen, G.-J., Zhang, G.-J., Zhou, Q., 2020. Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. Zoological. Res. 41, 1-11
|
Wang, Y., Li, J., Paterson, A.H., 2013. MCScanX-transposed:detecting transposed gene duplications based on multiple colinearity scans. Bioinformatics. 29, 1458-1460
|
Wang, Y., Tang, H., DeBarry, J.D., Tan, X., Li, J., Wang, X., Lee, T., Jin, H., Marler, B., Guo, H., et al., 2012. MCScanX:a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic. Acids. Res. 40, e49-e49
|
Wesolowski, T., 1994. On the Origin of Parental Care and the Early Evolution of Male and Female Parental Roles in Birds. Am. Nat. 143, 39-58
|
Wu, C.-I., Xu, E.Y., 2003. Sexual antagonism and X inactivation-the SAXI hypothesis. Trends. Genet. 19, 243-247
|
Xu, L., Auer, G., Peona, V., Suh, A., Deng, Y., Feng, S., Zhang, G., Blom, M.P.K., Christidis, L., Prost, S., Irestedt, et al., 2019a. Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds. Nat. Ecol. Evol. 3, 834-844
|
Xu, L., Sin, S.Y.W., Grayson, P., Edwards, S.V., Sackton, T.B., 2019b. Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds. Genome. Biol. Evol. 11, 2376-2390
|
Xu, L., Zhou, Q., 2020. The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized. Genes-basel. 11, 1126
|
Yang, Z., 2007. PAML 4:Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 1586-1591
|
Yazdi, H.P., Ellegren, H., 2018. A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution. Genome. Biol. Evol. 10, 2049-2060
|
Yonezawa, T., Segawa, T., Mori, H., Campos, P.F., Hongoh, Y., Endo, H., Akiyoshi, A., Kohno, N., Nishida, S., Wu, J., Jin, H., Adachi, et al., 2017. Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites. Curr. Biol. 27, 68-77
|
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D.M., Lee, C., Storz, J.F., Antunes, A., Greenwold, M.J., Meredith, R.W., et al., 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 346, 1311-1320
|
Zhang, J., Li, C., Zhou, Q., Zhang, G., 2015. Improving the ostrich genome assembly using optical mapping data. Gigascience. 4, 24
|
Zhang, Y.E., Vibranovski, M.D., Landback, P., Marais, G.A.B., Long, M., 2010. Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome. PLoS. Biol. 8, e1000494
|
Zhou, Q., Zhang, J., Bachtrog, D., An, N., Huang, Q., Jarvis, E.D., Gilbert, M.T.P., Zhang, G., 2014. Complex evolutionary trajectories of sex chromosomes across bird taxa. Science. 346, 1246338-1246338
|