Citation: | Zong-Ji Wang, Guang-Ji Chen, Guo-Jie Zhang, Qi Zhou. Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. Zoological Research, 2021, 42(1): 51-61. doi: 10.24272/j.issn.2095-8137.2020.175 |
[1] |
Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, et al. 2016. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered iberian lynx. Genome Biology, 17: 251. doi: 10.1186/s13059-016-1090-1
|
[2] |
Altimiras J, Lindgren I, Giraldo-Deck LM, Matthei A, Garitano-Zavala Á. 2017. Aerobic performance in tinamous is limited by their small heart. A novel hypothesis in the evolution of avian flight. Scientific Reports, 7(1): 15964.
|
[3] |
Angst D, Buffetaut E. 2017. Paleobiology of Giant Flightless Birds. Oxford: Elsevier.
|
[4] |
Barrón MG, Fiston-Lavier AS, Petrov DA, González J. 2014. Population genomics of transposable elements in Drosophila. Annual Review of Genetics, 48: 561−581. doi: 10.1146/annurev-genet-120213-092359
|
[5] |
Beißbarth T, Speed TP. 2004. GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics, 20(9): 1464−1465. doi: 10.1093/bioinformatics/bth088
|
[6] |
Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. 2001. Controlling the false discovery rate in behavior genetics research. Behavioural Brain Research, 125(1-2): 279−284. doi: 10.1016/S0166-4328(01)00297-2
|
[7] |
Berlin S, Tomaras D, Charlesworth B. 2007. Low mitochondrial variability in birds may indicate hill–robertson effects on the w chromosome. Heredity, 99(4): 389−396. doi: 10.1038/sj.hdy.6801014
|
[8] |
Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, et al. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69(2): 313−319. doi: 10.1016/j.ympev.2012.08.023
|
[9] |
Bishop CM. 1997. Heart mass and the maximum cardiac output of birds and mammals: Implications for estimating the maximum aerobic power input of flying animals. Philosophical Transactions of the Royal Society B: Biological Sciences, 352(1352): 447−456. doi: 10.1098/rstb.1997.0032
|
[10] |
Charlesworth B, Charlesworth D. 2000. The degeneration of Y chromosomes. Philosophical Transactions of the Royal Society B: Biological Sciences, 355(1403): 1563−1572. doi: 10.1098/rstb.2000.0717
|
[11] |
Churakov G, Grundmann N, Kuritzin A, Brosius J, Makałowski W, Schmitz J. 2010. A novel web-based tint application and the chronology of the primate alu retroposon activity. BMC Evolutionary Biology, 10: 376. doi: 10.1186/1471-2148-10-376
|
[12] |
De Bie T, Cristianini N, Demuth JP, Hahn MW. 2006. CAFE: a computational tool for the study of gene family evolution. Bioinformatics, 22(10): 1269−1271. doi: 10.1093/bioinformatics/btl097
|
[13] |
Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW. 2006. The evolution of mammalian gene families. PLoS One, 1(1): e85. doi: 10.1371/journal.pone.0000085
|
[14] |
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43(5): 491−498. doi: 10.1038/ng.806
|
[15] |
Hahn MW, Han MV, Han SG. 2007. Gene family evolution across 12 Drosophila genomes. PLoS Genetics, 3(11): e197. doi: 10.1371/journal.pgen.0030197
|
[16] |
Handford P, Mares MA. 1985. The mating systems of ratites and tinamous: an evolutionary perspective. Biological Journal of the Linnean Society, 25(1): 77−104. doi: 10.1111/j.1095-8312.1985.tb00387.x
|
[17] |
Houde P. 1986. Ostrich ancestors found in the northern hemisphere suggest new hypothesis of ratite origins. Nature, 324(6097): 563−565. doi: 10.1038/324563a0
|
[18] |
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215): 1320−1331. doi: 10.1126/science.1253451
|
[19] |
Kapusta A, Suh A, Feschotte C. 2017. Dynamics of genome size evolution in birds and mammals. Proceedings of the National Academy of Sciences of the United States of America, 114(8): E1460−E1469. doi: 10.1073/pnas.1616702114
|
[20] |
Kent WJ. 2002. BLAT—the BLAST-like alignment tool. Genome Research, 12(4): 656−664. doi: 10.1101/gr.229202
|
[21] |
Le Duc D, Renaud G, Krishnan A, Almén MS, Huynen L, Prohaska SJ, et al. 2015. Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biology, 16(1): 147. doi: 10.1186/s13059-015-0711-4
|
[22] |
Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, et al. 2006. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Research, 34(S1): D572−D580.
|
[23] |
Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature, 475(7357): 493−496. doi: 10.1038/nature10231
|
[24] |
Löytynoja A, Goldman N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences of the United States of America, 102(30): 10557−10562. doi: 10.1073/pnas.0409137102
|
[25] |
Lynch M. 2007. The Origins of Genome Architecture. Sunderland, MA: Sinauer Associates.
|
[26] |
Nadachowska-Brzyska K, Li C, Smeds L, Zhang GJ, Ellegren H. 2015. Temporal dynamics of avian populations during pleistocene revealed by whole-genome sequences. Current Biology, 25(10): 1375−1380. doi: 10.1016/j.cub.2015.03.047
|
[27] |
O’Connor RE, Farré M, Joseph S, Damas J, Kiazim L, Jennings R, et al. 2018. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biology, 19(1): 171. doi: 10.1186/s13059-018-1550-x
|
[28] |
Ogawa A, Murata K, Mizuno S. 1998. The location of Z-and W-linked marker genes and sequence on the homomorphic sex chromosomes of the ostrich and the emu. Proceedings of the National Academy of Sciences of the United States of America, 95(8): 4415−4418. doi: 10.1073/pnas.95.8.4415
|
[29] |
Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in r language. Bioinformatics, 20(2): 289−290. doi: 10.1093/bioinformatics/btg412
|
[30] |
Pigozzi MI. 1999. Origin and evolution of the sex chromosomes in birds. Biocell, 23(2): 79−95.
|
[31] |
Pigozzi MI, Solari AJ. 1999. The ZW pairs of two paleognath birds from two orders show transitional stages of sex chromosome differentiation. Chromosome Research, 7(7): 541−551. doi: 10.1023/A:1009241528994
|
[32] |
Sackton TB, Grayson P, Cloutier A, Hu ZR, Liu JS, Wheeler NE, et al. 2019. Convergent regulatory evolution and loss of flight in paleognathous birds. Science, 364(6435): 74−78. doi: 10.1126/science.aat7244
|
[33] |
Sackton TB, Lazzaro BP, Schlenke TA, Evans JD, Hultmark D, Clark AG. 2007. Dynamic evolution of the innate immune system in Drosophila. Nature Genetics, 39(12): 1461−1468. doi: 10.1038/ng.2007.60
|
[34] |
Shetty S, Griffin DK, Graves JAM. 1999. Comparative painting reveals strong chromosome homology over 80 million years of bird evolution. Chromosome Research, 7(4): 289−295. doi: 10.1023/A:1009278914829
|
[35] |
Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A, et al. 2015. Evolutionary analysis of the female-specific avian w chromosome. Nature Communications, 6: 7330. doi: 10.1038/ncomms8330
|
[36] |
Suh A, Paus M, Kiefmann M, Churakov G, Franke FA, Brosius J, et al. 2011. Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nature Communications, 2: 443. doi: 10.1038/ncomms1448
|
[37] |
Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, et al. 2016. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nature Communications, 7: 11396. doi: 10.1038/ncomms11396
|
[38] |
Takagi N, Itoh M, Sasaki M. 1972. Chromosome studies in four species of Ratitae (Aves). Chromosoma, 36(3): 281−291.
|
[39] |
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56(4): 564−577. doi: 10.1080/10635150701472164
|
[40] |
Tsuda Y, Nishida-Umehara C, Ishijima J, Yamada K, Matsuda Y. 2007. Comparison of the z and w sex chromosomal architectures in elegant crested tinamou (Eudromia elegans) and ostrich (Struthio camelus) and the process of sex chromosome differentiation in palaeognathous birds. Chromosoma, 116(2): 159−173. doi: 10.1007/s00412-006-0088-y
|
[41] |
Wang ZJ, Zhang JL, Xu XM, Witt C, Deng Y, Chen GJ, et al. 2019. Phylogeny, transposable element and sex chromosome evolution of the basal lineage of birds. bioRxiv. doi: 10.1101/750109.
|
[42] |
Wright NA, Gregory TR, Witt CC. 2014. Metabolic ‘engines’ of flight drive genome size reduction in birds. Proceedings of the Royal Society B: Biological Sciences, 281(1779): 20132780. doi: 10.1098/rspb.2013.2780
|
[43] |
Yang ZH. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8): 1586−1591. doi: 10.1093/molbev/msm088
|
[44] |
Young JJ, Grayson P, Edwards SV, Tabin CJ. 2019. Attenuated fgf signaling underlies the forelimb heterochrony in the emu Dromaius novaehollandiae. Current Biology, 29(21): 3681−3691.e5. doi: 10.1016/j.cub.2019.09.014
|
[45] |
Zhang GJ, Li C, Li QY, Li B, Larkin DM, Lee C, et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215): 1311−1320. doi: 10.1126/science.1251385
|
[46] |
Zhou Q, Zhang JL, Bachtrog D, An N, Huang QF, Jarvis ED, et al. 2014. Complex evolutionary trajectories of sex chromosomes across bird taxa. Science, 346(6215): 1246338. doi: 10.1126/science.1246338
|
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