Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses

Genome Biology and Evolution

Volumn 7, Issue 7, 2015, Pages 2010-2022

  Bidon, Tobias ^a,b   Schreck, Nancy ^a   Hailer, Frank ^a,c   Nilsson, Maria A ^a   Janke, Axel ^a,d  

^a BIODIVERSITY AND CLIMATE RESEARCH CENTRE BIK F   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c CARDIFF UNIVERSITY   (United Kingdom)

^d GOETHE UNIVERSITY   (Germany)

Author keywords

divergence; male inheritance; patriline; sex chromosome; Ursidae; Y chromosome

Indexed keywords

ANIMAL; BEAR; CLASSIFICATION; FEMALE; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; MALE; MOLECULAR EVOLUTION; NUCLEOTIDE REPEAT; PHYLOGENY; Y CHROMOSOME;

ANIMALS; EVOLUTION, MOLECULAR; FEMALE; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MALE; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID; URSIDAE; Y CHROMOSOME;

EID: 84964694545     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv103     Document Type: Article

References (71)

1. Anderson S, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
2. Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data.
3. Bachtrog D. 2013. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nat Rev Genet. 14:113-124.
4. Bellott DW, et al. 2014. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508:494-499.
5. Bidon T, et al. 2013. A sensitive and specific multiplex PCR approach for sex identification of ursine and tremarctine bears suitable for non-invasive samples. Mol Ecol Resour. 13:362-368.
6. Bidon T, et al. 2014. Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages. Mol Biol Evol. 31:1353-1363.
7. Bouckaert R, et al. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 10:e1003537.
8. Cahill JA, et al. 2013. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genet. 9:e1003345.
9. Cahill JA, et al. 2015. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol. 24:1205-1217.
10. Carvalho AB, Clark AG. 2013. Efficient identification of Y chromosome sequences in the human and Drosophila genomes. Genome Res. 23:1894-1907.
11. Carvalho AB, et al. 2003. Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go? Genetica 117:227-237.
12. Carvalho AB, Koerich LB, Clark AG. 2009. Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet. 25:270-277.
13. Carvalho AB, Lazzaro BP, Clark AG. 2000. Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides. Proc Natl Acad Sci U S A. 97:13239-13244.
14. Chen N, Bellott DW, Page DC, Clark AG. 2012. Identification of avian W-linked contigs by short-read sequencing. BMC Genomics 13:183.
15. Chen S, et al. 2014. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet. 46:253-260.
16. Chesser RK, Baker RJ. 1996. Effective sizes and dynamics of uniparentally and diparentally inherited genes. Genetics 144:1225-1235.
17. Clement M, Posada D, Crandall K. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol. 9:1657-1659.
18. Cortez D, et al. 2014. Origins and functional evolution of Y chromosomes across mammals. Nature 508:488-493.
19. Cronin MA, et al. 2014. Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) derived from genome sequences. J Hered. 105:312-323.
20. Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9:772.
21. Flagstad Ø, Røed KH. 2003. Refugial origins of reindeer (Rangifer tarandus L.) inferred from mitochondrial DNA sequences. Evolution 57:658-670.
22. Fu Q, et al. 2014. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514:445-449.
23. Greminger MP, Krützen M, Schelling C, Pienkowska-Schelling A, Wandeler P. 2010. The quest for Y-chromosomal markers - methodological strategies for mammalian non-model organisms. Mol Ecol Resour. 10:409-420.
24. Hailer F, et al. 2012. Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336:344-347.
25. Hall AB, et al. 2013. Six novel Y chromosome genes in Anopheles mosquitoes discovered by independently sequencing males and females. BMC Genomics 14:273.
26. Hallast P, Balaresque P, Bowden GR, Ballereau S, Jobling M. 2013. Recombination dynamics of a human Y-chromosomal palindrome: rapid GC-biased gene conversion, multi-kilobase conversion tracts, and rare inversions. PLoS Genet. 9:e1003666.
27. Hughes JF, et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536-539.
28. Hughes JF, et al. 2012. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature 483:82-86.
29. Hughes JF, Rozen S. 2012. Genomics and genetics of human and primate Y chromosomes. Annu Rev Genomics Hum Genet. 13:83-108.
30. Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254-267.
31. Janke A, Feldmaier-Fuchs G, Thomas WK, von Haeseler A, Pääbo S. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243-256.
32. Jobling M, Tyler-Smith C. 2003. The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet. 4:598-612.
33. Joshi NA, Fass JN. 2011. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. Available from: https://github.com/najoshi/sickle
34. Kayser M. 2007. Uni-parental markers in human identity testing including forensic DNA analysis. Biotechniques 43:Sxv-Sxxi.
35. Kondo M, et al. 2006. Genomic organization of the sex-determining and adjacent regions of the sex chromosomes of medaka. Genome Res. 16:815-826.
36. Krzywinski J, Nusskern DR, Kern MK, Besansky NJ. 2004. Isolation and characterization of Y chromosome sequences from the African malaria mosquito Anopheles gambiae. Genetics 166:1291-1302.
37. Kurtén B, Anderson E.1980. Pleistocene mammals of North America. New York: Columbia University Press.
38. Kutschera VE, et al. 2014. Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow. Mol Biol Evol. 31:2004-2017.
39. Kvikstad EM, Makova KD. 2010. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res. 20:600-613.
40. Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
41. Li B, Zhang G, Willerslev E, Wang J. 2011. Genomic data from the Polar Bear (Ursus maritimus). Gigascience. Available from: http://dx.doi.org/10.5524/100008
42. Li G, et al. 2013. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution. Genome Res. 23:1486-1495.
43. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
44. Li H, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
45. Liu S, et al. 2014. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 157:785-794.
46. McKenna A, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-1303.
47. Miller W, et al. 2012. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc Natl Acad Sci U S A. 109:E2382-E2390.
48. Murphy WJ, et al. 2006. Novel gene acquisition on carnivore Y chromosomes. PLoS Genet. 2:e43.
49. Nakagome S, Pecon-Slattery J, Masuda R. 2008. Unequal rates of Y chromosome gene divergence during speciation of the family Ursidae. Mol Biol Evol. 25:1344-1356.
50. O'Brien S, Menninger J, Nash W. 2006. Atlas of mammalian chromosomes. Hoboken (NJ): John Wiley & Sons.
51. Pagès M, et al. 2008. Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny. Mol Phylogenet Evol. 47:73-83.
52. Pagès M, et al. 2009. A system for sex determination from degraded DNA: a useful tool for palaeogenetics and conservation genetics of ursids. Conserv Genet. 10:897-907.
53. Posada D, Crandall K, Holmes EC. 2002. Recombination in evolutionary genomics. Annu Rev Genet. 36:75-97.
54. Rogers J, Gibbs R. 2014. Comparative primate genomics: emerging patterns of genome content and dynamics. Nat Rev Genet. 15:347-359.
55. Ross MT, et al. 2005. The DNA sequence of the human X chromosome. Nature 434:325-337.
56. Rosser ZH, Balaresque P, Jobling M. 2009. Gene conversion between the X chromosome and the male-specific region of the Y chromosome at a translocation hotspot. Am J Hum Genet. 85:130-134.
57. Sacks BN, et al. 2013. Y chromosome analysis of dingoes and southeast asian village dogs suggests a neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals. Mol Biol Evol. 30:1103-1118.
58. Scozzari R, et al. 2014. An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa. Genome Res. 24:535-544.
59. Skaletsky H, et al. 2003. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423:825-837.
60. Slattery JP, Sanner-wachter L, O'Brien SJ. 2000. Novel gene conversion between X-Y homologues located in the nonrecombining region of the Y chromosome in Felidae (Mammalia). Proc Natl Acad Sci U S A. 97:5307-5312.
61. Smit AFA, Riggs AD. 1995. MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res. 23:98-102.
62. Smit AFA, Hubley R, Green P. 1996. RepeatMasker Open-3.0. 1996-2010 'http://www.repeatmasker.org'.
63. Soh YQS, et al. 2014. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell 159:800-813.
64. Trombetta B, Sellitto D, Scozzari R, Cruciani F. 2014. Inter- and intraspecies phylogenetic analyses reveal extensive X-Y gene conversion in the evolution of gametologous sequences of human sex chromosomes. Mol Biol Evol. 31:2108-2123.
65. Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau MHD. 2014. Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome. Hum Mutat. 35:187-191.
66. Veeramah KR, Hammer MF. 2014. The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet. 15:149-162.
67. Wallner B, et al. 2013. Identification of genetic variation on the horse Y chromosome and the tracing of male founder lineages in modern breeds. PLoS One 8:e60015.
68. Walters-Conte KB, Johnson DLE, Allard MW, Pecon-Slattery J. 2011. Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact. J Hered. 102(Suppl.):S2-S10.
69. Wei W, et al. 2013. A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res. 23:388-395.
70. Willard HF. 2003. Tales of the Y chromosome. Nature 423:810-813.
71. Wilson AC, et al. 1985. Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc. 26:375-400.