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Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Murray, Gemma G. R., Soares, André E. R., Novak, Ben J., Schaefer, Nathan K., Cahill, James A., Baker, Allan J., Demboski, John R., Doll, Andrew, Da Fonseca, Rute R., Fulton, Tara L., Gilbert, M. Thomas P., Heintzman, Peter D., Letts, Brandon, McIntosh, George, O’Connell, Brendan L., Peck, Mark, Pipes, Marie-Lorraine, Rice, Edward S., Santos, Kathryn M., Sohrweide, A. Gregory, Vohr, Samuel H., Corbett-Detig, Russell B., Green, Richard E., Shapiro, Beth·2017·Science
DOI 10.1126/science.aao0960

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Abstract

Genetics of the passenger pigeon: The now-extinct passenger pigeon used to be one of the most numerous vertebrates on Earth. Murray et al. examined the genomes of four passenger pigeon samples from different locales within its range. They describe the interplay between passenger pigeon population size, genome structure and recombination, and natural selection. They conclude that a reduction in genetic diversity provided few avenues for the bird to respond to human pressures, which ultimately drove it to extinction. Science , this issue p. 951

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Crossref · 10.1126/science.aao0960

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  • Complete genome data from single diploid individuals and/or populations provide new avenues for reconstructing paleodemographic trajectories using PSMC and MSMC.

    “Complete genome data from single diploid individuals and/or populations have provided new avenues for reconstructing paleodemographic trajectories using the pairwise and multiple sequentially Markovian coalescent (PSMC 317 and MSMC 318 , respectively) modelling frameworks.”

    From Ancient DNA analysis (2021) · cites this paper as [318]

    In section 3 (page not provided), the paper describes an earlier use of PSMC on a passenger pigeon nuclear genome to infer population history. It does not discuss MSMC, and it cautions that PSMC may be unreliable for this genome because selection affects genome-wide diversity. Thus it supports the PSMC part of the general statement, but not the attribution of both frameworks to this source. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 116

  1. E. H. Bucher “The causes of extinction of the Passenger Pigeon” in Current Ornithology D. M. Power Ed. (Springer US 1992) Current Ornithology pp. 1–36. · DOI
  2. 10.1038/nrg2526 · DOI
  3. 10.1017/S0016672300014634 · DOI · Paper page
  4. 10.1038/356519a0 · DOI
  5. 10.1093/genetics/155.2.909 · DOI
  6. 10.1534/genetics.111.134288 · DOI
  7. R. C. Lewontin The Genetic Basis of Evolutionary Change (Columbia University Press 1974).
  8. 10.1371/journal.pbio.1002112 · DOI
  9. 10.1371/journal.pbio.1001388 · DOI
  10. 10.1016/j.ympev.2010.05.010 · DOI
  11. 10.1016/j.tree.2009.12.004 · DOI
  12. 10.1146/annurev.genet.42.110807.091442 · DOI
  13. 10.1038/351652a0 · DOI
  14. B. T. Grenfell A. P. Dobson Ecology of Infectious Diseases in Natural Populations (Cambridge University Press 1995). · DOI
  15. 10.1111/j.1365-2435.2012.02029.x · DOI
  16. 10.1017/S0016672300010156 · DOI · Paper page
  17. 10.1111/mec.14083 · DOI
  18. 10.1098/rspb.2016.2756 · DOI
  19. 10.1186/gb-2010-11-6-r68 · DOI
  20. 10.1093/gbe/evu157 · DOI
  21. 10.1093/molbev/msv214 · DOI
  22. 10.1016/j.gene.2006.04.030 · DOI
  23. 10.1126/science.289.5482.1139b · DOI
  24. 10.1111/j.1755-0998.2009.02824.x · DOI
  25. 10.1007/978-1-61779-516-9_4 · DOI
  26. 10.1126/science.295.5560.1683 · DOI
  27. T. L. Fulton M. Stiller “PCR Amplification Cloning and Sequencing of Ancient DNA” in Ancient DNA B. Shapiro M. Hofreiter Eds. (Humana Press) Methods in Molecular Biology pp. 111–119 (2012). · DOI
  28. 10.1101/gr.128124.111 · DOI
  29. 10.1101/pdb.prot5448 · DOI
  30. 10.1186/s12862-016-0800-3 · DOI
  31. 10.1371/journal.pone.0056301 · DOI
  32. 10.1093/nar/gkh340 · DOI · Paper page
  33. 10.1093/molbev/msp259 · DOI
  34. 10.1111/j.1755-0998.2010.02847.x · DOI
  35. 10.1111/j.1755-0998.2010.02890.x · DOI
  36. 10.1093/molbev/mss075 · DOI
  37. 10.1093/molbev/msi103 · DOI
  38. 10.1111/j.1755-0998.2011.02988.x · DOI
  39. 10.1111/mec.13780 · DOI
  40. 10.1016/j.tig.2005.11.006 · DOI
  41. 10.1126/science.1122033 · DOI
  42. 10.1371/journal.pone.0023501 · DOI
  43. 10.1101/gr.193474.115 · DOI · Paper page
  44. 10.1186/gb-2013-14-4-r36 · DOI · Paper page
  45. 10.1093/nar/gkl200 · DOI · Paper page
  46. 10.1093/nar/25.17.3389 · DOI · Paper page
  47. H. Li Aligning sequence reads clone sequences and assembly contigs with BWA-MEM. arXiv [q-bio.GN] (2013); https://arxiv.org/abs/1303.3997. · arXiv
  48. 10.1093/bioinformatics/btp324 · DOI · Paper page
  49. 10.1093/bioinformatics/btq033 · DOI · Paper page
  50. 10.1038/ng.806 · DOI
  51. 10.1093/bioinformatics/btr330 · DOI
  52. 10.1093/nar/30.11.2478 · DOI · Paper page
  53. 10.1093/bioinformatics/btg412 · DOI · Paper page
  54. 10.1534/genetics.112.142018 · DOI
  55. P. D. Heintzman, A. E. R. Soares, D. Chang, B. Shapiro, Paleogenomics. Rev. Cell Biol. Mol. Med. 1, 243–267 (2015).
  56. 10.1371/journal.pgen.1000698 · DOI
  57. 10.1093/gbe/evs027 · DOI
  58. 10.1093/molbev/msq249 · DOI
  59. 10.1073/pnas.0610385104 · DOI
  60. 10.1093/oxfordjournals.molbev.a004201 · DOI
  61. 10.1016/0378-1119(90)90491-9 · DOI
  62. 10.1093/genetics/139.2.1067 · DOI
  63. 10.1006/jmbi.1996.0528 · DOI
  64. 10.1101/gr.101410.109 · DOI
  65. 10.1111/mec.12810 · DOI
  66. 10.1126/science.aad0843 · DOI
  67. 10.1101/gr.6386707 · DOI
  68. 10.1534/genetics.112.141036 · DOI
  69. 10.1038/nature10231 · DOI · Paper page
  70. 10.1534/genetics.116.190223 · DOI
  71. 10.1017/S0016672308009695 · DOI
  72. 10.1002/ece3.329 · DOI
  73. 10.1371/journal.pgen.1000987 · DOI
  74. 10.1111/j.0014-3820.2001.tb00732.x · DOI
  75. 10.1371/journal.pgen.1004222 · DOI
  76. 10.1016/j.biocon.2014.09.023 · DOI
  77. 10.1038/nature11584 · DOI
  78. 10.1126/science.1251385 · DOI · Paper page
  79. 10.1093/nar/28.1.27 · DOI · Paper page
  80. 10.1093/molbev/msn005 · DOI
  81. 10.1073/pnas.1605660114 · DOI
  82. 10.1017/S0016672302005955 · DOI
  83. 10.1534/genetics.104.033795 · DOI
  84. 10.1093/genetics/123.3.597 · DOI
  85. 10.1093/genetics/155.3.1405 · DOI · Paper page
  86. 10.1126/science.1188021 · DOI · Paper page
  87. 10.1093/molbev/msr048 · DOI · Paper page
  88. 10.1073/pnas.1220835110 · DOI
  89. 10.1126/science.1172873 · DOI · Paper page
  90. 10.1002/eji.200939896 · DOI
  91. 10.1128/JVI.73.10.8696-8702.1999 · DOI
  92. 10.4067/S0716-97602011000100011 · DOI
  93. 10.1016/j.neuropharm.2007.07.005 · DOI
  94. 10.1016/j.neuropharm.2007.08.011 · DOI
  95. 10.1647/2014-034 · DOI
  96. 10.1371/journal.pone.0126736 · DOI
  97. 10.1016/j.ajhg.2013.11.017 · DOI · Paper page
  98. 10.1096/fj.10-157412 · DOI
  99. 10.1371/journal.pone.0025344 · DOI
  100. 10.1093/jn/133.3.707 · DOI
  101. 10.1016/j.atherosclerosis.2009.01.004 · DOI · Paper page
  102. 10.1016/j.cell.2014.03.054 · DOI · Paper page
  103. 10.1016/j.cbpb.2005.10.009 · DOI
  104. 10.1186/1471-2164-11-13 · DOI
  105. 10.2337/diabetes.53.4.1141 · DOI
  106. 10.1083/jcb.200108007 · DOI
  107. 10.1126/science.1169123 · DOI
  108. 10.1038/ng.2765 · DOI
  109. 10.1002/med.21286 · DOI
  110. 10.1007/s00439-005-0019-7 · DOI
  111. 10.1016/j.gene.2013.12.055 · DOI
  112. 10.1007/s00424-006-0047-8 · DOI
  113. 10.1186/1471-2105-11-170 · DOI
  114. 10.1186/1471-2350-11-41 · DOI
  115. 10.1099/vir.0.012401-0 · DOI
  116. 10.1093/molehr/gaq029 · DOI

Cited by

Sorted by citations

  • Ancient DNA analysis

    Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411

Metadata

Authors
Murray, G. G. R., Soares, A. E. R., Novak, B. J., Schaefer, N. K., Cahill, J. A., Baker, A. J., Demboski, J. R., Doll, A., Da Fonseca, R. R., Fulton, T. L., Gilbert, M. T. P., Heintzman, P. D., Letts, B., McIntosh, G., O’Connell, B. L., Peck, M., Pipes, M.-L., Rice, E. S., Santos, K. M., Sohrweide, A. G., Vohr, S. H., Corbett-Detig, R. B., Green, R. E., & Shapiro, B.
Affiliations
  • Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.
  • Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
  • Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada.
  • Department of Zoology, Denver Museum of Nature and Science, Denver, CO 80205, USA.
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
  • Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
  • Collections Department, Rochester Museum and Science Center, Rochester, NY 14607, USA.
  • Marie-Lorraine Pipes, Zooarchaeologist Consultant, Victor, NY 14564, USA.
  • A. Gregory Sohrweide D.D.S., Baldwinsville, NY 13027, USA.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2017-11-17
Volume
358
Issue
6365
Pages
951-954
ISSN
  • 0036-8075
  • 1095-9203
DOI
10.1126/science.aao0960
Cited by
132
References
9
Language
en
Funders
  • David and Lucile Packard Foundation
  • Gordon and Betty Moore Foundation
  • Revive & Restore
  • Ciência sem Fronteiras fellowship - CAPES, Brazil

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