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  1. Method: Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
    • John E. McCormack,
    • Brant C. Faircloth,
    • Nicholas G. Crawford,
    • Patricia Adair Gowaty,
    • Robb T. Brumfield,
    • and Travis C. Glenn
    Genome Res. April 2012 22: 746-754; Published in Advance December 29, 2011, doi:10.1101/gr.125864.111
    ...and Xenarthra (Hallstro¨m et al. 2007; Murphy et al. 2007; Wildman et al. 2007), which has been used to validate the importance to placental mammal evolution of a major North–South split caused by the break-up of Pangaea into Gondwana and Laurasia during the Cretaceous (Wildman et al. 2007). Retroposon studies...
  2. LETTER: Characterization of intron loss events in mammals
    • Jasmin Coulombe-Huntington and
    • Jacek Majewski
    Genome Res. January 2007 17: 23-32; Published in Advance November 15, 2006, doi:10.1101/gr.5703406
    ...in the Exon-Intron Database (EID) Brief. Bioinform. 7 : 178 – 185 . ↵ Siepel, A. , Haussler, D. ( 2004 ) Combining phylogenetic and hidden Markov models in biosequence analysis . J. Comput. Biol. 11 : 413 – 428 . ↵ Springer, M.S. , Murphy, W.J. , Eizirik, E. , O’Brien, S.J. ( 2003 ) Placental mammal...
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  3. ARTICLE: Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
    • Shan Yang,
    • Arian F. Smit,
    • Scott Schwartz,
    • Francesca Chiaromonte,
    • Krishna M. Roskin,
    • David Haussler,
    • Webb Miller,
    • and Ross C. Hardison
    Genome Res. April 2004 14: 517-527; doi:10.1101/gr.1984404
    ...Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes Shan Yang 1 , Arian F. Smit 4 , Scott Schwartz 2 , Francesca Chiaromonte 3 , Krishna M. Roskin 5 , David Haussler 5 , 6...
  4. Platypus Special/Letter: Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs
    • Jürgen Schmitz,
    • Anja Zemann,
    • Gennady Churakov,
    • Heiner Kuhl,
    • Frank Grützner,
    • Richard Reinhardt,
    • and Jürgen Brosius
    Genome Res. June 2008 18: 1005-1010; Published in Advance May 7, 2008, doi:10.1101/gr.7177908
    ...retroposons. In mammals the activity of L1 elements is restricted to therians (placentals and marsupials). To date, no L1 activity has been demonstrated for monotremes ( Kordis et al. 2006 ); thus, L1-mediated co-retroposition of RNAs is also expected to be restricted to therian mammals. In monotremes...
  5. Research: Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes
    • Jonathan Romiguier,
    • Vincent Ranwez,
    • Emmanuel J.P. Douzery,
    • and Nicolas Galtier
    Genome Res. August 2010 20: 1001-1009; Published in Advance June 7, 2010, doi:10.1101/gr.104372.109
    ...of genes. The intensively studied apes and (especially) murids do not reflect the general placental pattern. We correlated GC-content evolution with species life-history traits and cytology. Significant effects of body mass and genome size were detected, with each being consistent with the GC-biased gene...
  6. PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
    • Paul B. Samollow
    Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
    ...and the fundamental biologic characteristics of metatherians that distinguish them from other mammalian species. Metatherian and eutherian (placental) mammals are more closely related to one another than to other vertebrate groups, and owing to this close relationship they share fundamentally similar genetic...
  7. LETTER: Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs)
    • Maren Krull,
    • Mirjan Petrusma,
    • Wojciech Makalowski,
    • Jürgen Brosius,
    • and Jürgen Schmitz
    Genome Res. August 2007 17: 1139-1145; Published in Advance July 10, 2007, doi:10.1101/gr.6320607
    ...mammalian evolution. Four of these are expressed as alternatively spliced transcripts; three in species throughout the mammalian phylogenetic tree and one solely in primates. The fifth is the first experimentally verified, constitutively expressed retroposed SINE element in mammals. This pattern of highly...
  8. Research: LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
    • Shengjun Tan,
    • Margarida Cardoso-Moreira,
    • Wenwen Shi,
    • Dan Zhang,
    • Jiawei Huang,
    • Yanan Mao,
    • Hangxing Jia,
    • Yaqiong Zhang,
    • Chunyan Chen,
    • Yi Shao,
    • Liang Leng,
    • Zhonghua Liu,
    • Xun Huang,
    • Manyuan Long,
    • and Yong E. Zhang
    Genome Res. December 2016 26: 1663-1675; Published in Advance October 20, 2016, doi:10.1101/gr.204925.116
    ...; Supplemental Table 5; Witherspoon et al. 2010). With these additional data, we identified 18 insertion sites for nine retrocopies (Table 2; Supplemental Table 6). Twelve insertion sites were further validated by PCR followed by Sanger sequencing. In agreement with the biased insertion pattern of LTR...
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  9. PERSPECTIVE: Raising the estimate of functional human sequences
    • Michael Pheasant and
    • John S. Mattick
    Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
    .../or trafficked to specific subcellular locations, as well as exhibit subtle evidence of selection. On the other hand, analyses of conservation patterns indicate that only ∼5% (3%–8%) of the human genome is under purifying selection for functions common to mammals. However, these estimates rely on the assumption...
  10. Research: Speciation network in Laurasiatheria: retrophylogenomic signals
    • Liliya Doronina,
    • Gennady Churakov,
    • Andrej Kuritzin,
    • Jingjing Shi,
    • Robert Baertsch,
    • Hiram Clawson,
    • and Jürgen Schmitz
    Genome Res. June 2017 27: 997-1003; Published in Advance March 15, 2017, doi:10.1101/gr.210948.116
    ...retroposon insertion patterns in placental mammals. Genome Res 19: 868–875. Doronina L, Churakov G, Shi J, Brosius J, Baertsch R, Clawson H, Schmitz J. 2015. Exploring massive incomplete lineage sorting in arctoids (Laurasiatheria, Carnivora). Mol Biol Evol 32: 3194–3204. Ebersberger I, Galgoczy P, Taudien S...
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