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The nature of the last universal common ancestor.
Penny D, Poole A. Penny D, et al. Curr Opin Genet Dev. 1999 Dec;9(6):672-7. doi: 10.1016/s0959-437x(99)00020-9. Curr Opin Genet Dev. 1999. PMID: 10607605 Review.
An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics.
Hoeppner MP, Denisenko E, Gardner PP, Schmeier S, Poole AM. Hoeppner MP, et al. Mol Biol Evol. 2018 Jun 1;35(6):1451-1462. doi: 10.1093/molbev/msy046. Mol Biol Evol. 2018. PMID: 29617896 Free PMC article.
Mammalian diversification has coincided with a rapid proliferation of various types of noncoding RNAs, including members of both snRNAs and snoRNAs. ...Projects such as ENCODE and FANTOM have revealed a hidden world of genomic expression patterns, as well as a
Mammalian diversification has coincided with a rapid proliferation of various types of noncoding RNAs, including members of both snRN …
An overview of the introns-first theory.
Penny D, Hoeppner MP, Poole AM, Jeffares DC. Penny D, et al. J Mol Evol. 2009 Nov;69(5):527-40. doi: 10.1007/s00239-009-9279-5. Epub 2009 Sep 24. J Mol Evol. 2009. PMID: 19777149
We review the introns-first hypothesis a decade after it was first proposed. It is that exons emerged from non-coding regions interspersed between RNA genes in an early RNA world, and is a subcomponent of a more general 'RNA-continuity' hypothesis. ...There i …
We review the introns-first hypothesis a decade after it was first proposed. It is that exons emerged from non-coding regions intersp …
Using ancestral sequences to uncover potential gene homologues.
Collins LJ, Poole AM, Penny D. Collins LJ, et al. Appl Bioinformatics. 2003;2(3 Suppl):S85-95. Appl Bioinformatics. 2003. PMID: 15130821
Ancestral sequences are inferred by aligning gene homologues on a known tree and estimating the most likely amino acid for each position at each node in that tree. ...Overall, including ancestral sequences in searches with BLAST and/or HMMER was the most successful approac …
Ancestral sequences are inferred by aligning gene homologues on a known tree and estimating the most likely amino acid for each posit …
Spliceosomal introns in Trichomonas vaginalis revisited.
Wang SE, Amir AS, Nguyen T, Poole AM, Simoes-Barbosa A. Wang SE, et al. Parasit Vectors. 2018 Nov 27;11(1):607. doi: 10.1186/s13071-018-3196-7. Parasit Vectors. 2018. PMID: 30482228 Free PMC article.
Despite having an unusually large genome and a rich gene repertoire among protists, spliceosomal introns in T. vaginalis appear rare: only 62 putative introns have been annotated in this genome, and little or no experimental evidence exists to back up these predictions. .. …
Despite having an unusually large genome and a rich gene repertoire among protists, spliceosomal introns in T. vaginalis appear rare: …
Relics from the RNA world.
Jeffares DC, Poole AM, Penny D. Jeffares DC, et al. J Mol Evol. 1998 Jan;46(1):18-36. doi: 10.1007/pl00006280. J Mol Evol. 1998. PMID: 9419222 Review.
Despite the constraints placed on its size by a low fidelity of replication (the Eigen limit), we conclude that the genome of this organism reached a considerable level of complexity that included several RNA-processing steps. ...Overall, this requires that such an …
Despite the constraints placed on its size by a low fidelity of replication (the Eigen limit), we conclude that the genome of this or …
The path from the RNA world.
Poole AM, Jeffares DC, Penny D. Poole AM, et al. J Mol Evol. 1998 Jan;46(1):1-17. doi: 10.1007/pl00006275. J Mol Evol. 1998. PMID: 9419221 Review.
By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that incorporated triplets of oligonucleotides. ...Many features of the model for the genome …
By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribo …
Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis.
Poole AM, Neumann N. Poole AM, et al. Res Microbiol. 2011 Jan;162(1):71-6. doi: 10.1016/j.resmic.2010.10.002. Epub 2010 Oct 27. Res Microbiol. 2011. PMID: 21034814
We show that placing phylogenetic results within a stem-and-crown framework eliminates such incompatibilities, and that an archaeal origin for eukaryotes (as suggested from recent phylogenies) can be uncontroversially reconciled with phagocytosis as the mechanism for engul …
We show that placing phylogenetic results within a stem-and-crown framework eliminates such incompatibilities, and that an archaeal o …
Horizontal gene transfer and the earliest stages of the evolution of life.
Poole AM. Poole AM. Res Microbiol. 2009 Sep;160(7):473-80. doi: 10.1016/j.resmic.2009.07.009. Epub 2009 Jul 30. Res Microbiol. 2009. PMID: 19647074 Review.
Evaluating hypotheses for the origin of eukaryotes.
Poole AM, Penny D. Poole AM, et al. Bioessays. 2007 Jan;29(1):74-84. doi: 10.1002/bies.20516. Bioessays. 2007. PMID: 17187354 Review.
Numerous scenarios explain the origin of the eukaryote cell by fusion or endosymbiosis between an archaeon and a bacterium (and sometimes a third partner). ...Can the data be explained by the null hypothesis that new features arise sequentially along a stem l …
Numerous scenarios explain the origin of the eukaryote cell by fusion or endosymbiosis between an archaeon and a bacterium (and somet …
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