Resolution of a deep animal divergence by the pattern of intron conservationScott William Roy
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 102:4403-8. 2005
..We find that only the ecdysozoa grouping satisfies these predictions, with P < 10(-6). Simulations show that our method, unlike some previous methods, is largely insensitive to rate variation between branches...
- Intron length distributions and gene prediction
Scott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Nucleic Acids Res 35:4737-42. 2007
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- Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans
Qi Zhou
CAS Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
BMC Genomics 13:109. 2012
..12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility...
- Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
Manuel Irimia
Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
BMC Evol Biol 7:188. 2007
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- The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification
David Hoogewijs
Department of Biology and Center for Molecular Phylogeny and Evolution, Ghent University, B 9000 Ghent, Belgium
BMC Evol Biol 8:279. 2008
..In silico analysis of the genome of Caenorhabditis elegans revealed an unexpectedly high number of globin genes featuring a remarkable diversity in gene structure, amino acid sequence and expression profiles...
- Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mol Biol Evol 25:1192-8. 2008
..Finally, we find a lack of synapomorphic gene losses, suggesting a low rate of ancestral gene loss in Plasmodium...
Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thalianaScott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 24:171-81. 2007
..This pattern implies that rates of intron creation were higher during earlier periods of evolution and further focuses attention on the causes of initial intron proliferation...
- A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain
Scott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 24:1447-57. 2007
..These results also provide evidence that multiple intron insertion into the same site is rare, further supporting the notion that early eukaryotic ancestors were very intron rich...
- Evolutionary conservation of UTR intron boundaries in Cryptococcus
Scott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 24:1140-8. 2007
..These results focus attention on the functional roles of eukaryotic UTRs and deepen the mystery of UTR intron splicing...
- On the incidence of intron loss and gain in paralogous gene families
Scott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 24:1579-81. 2007
..Statistical reanalysis of the data suggests, instead, that intron losses have outnumbered intron gains in paralogous gene families...
- Widespread intron loss suggests retrotransposon activity in ancient apicomplexans
Scott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 24:1926-33. 2007
..By contrast, Cryptosporidium introns are less evolutionary conserved with Toxoplasma than are introns from other apicomplexans; thus the few remaining introns are not simply indispensable ancestral introns...
When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysisScott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Bioessays 30:601-5. 2008
..Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html)...
- Rare genomic characters do not support Coelomata: intron loss/gain
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mol Biol Evol 25:620-3. 2008
..2005a. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408.). Instead, we show that our conclusions are likely to be robust to such concerns...
- Intron mis-splicing: no alternative?
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA
Genome Biol 9:208. 2008
..This striking inefficiency deepens the mystery of the proliferation and persistence of introns...
- Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
Scott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Genome Res 16:1270-5. 2006
..We suggest that intron loss/gain in some eukaryotic lineages may be concentrated in relatively short episodes coincident with occasional TE invasions...
- Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses
Scott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 23:2259-62. 2006
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- Intron-rich ancestors
Scott W Roy
Allan Wilson Centre, Massey University, Palmerston North, New Zealand
Trends Genet 22:468-71. 2006
..These results refocus our attention on the evolutionary history and importance of introns in early eukaryotic evolution...
- Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number
Scott William Roy
Department of Organismic and Evolutionary Biology, Harvard, Cambridge, Massachusetts 02138, USA
Genome Res 16:750-6. 2006
..The observed pattern suggests that the availability of stochastic intron loss and gain mutations can be a major determinant of changes in intron number...
- The evolution of spliceosomal introns: patterns, puzzles and progress
Scott William Roy
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Nat Rev Genet 7:211-21. 2006
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- Coevolution of genomic intron number and splice sites
Manuel Irimia
Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
Trends Genet 23:321-5. 2007
..It seems that eukaryotic ancestors had relatively large intron numbers and 'weak' 5'ss, a pattern associated with frequent alternative splicing in modern organisms...
- The pattern of intron loss
Scott W Roy
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 102:713-8. 2005
..Our results support a reverse transcriptase-mediated model of intron loss...
- Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain
Scott W Roy
Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 100:7158-62. 2003
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- Complex early genes
Scott W Roy
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 102:1986-91. 2005
..Intron losses outnumber gains over a large range of eukaryotic lineages. These results show that early eukaryotic gene structures were very complex, and that simplification, not embellishment, has dominated subsequent evolution...
- Sequence diversity and evolutionary dynamics of the dimorphic antigen merozoite surface protein-6 and other Msp genes of Plasmodium falciparum
Scott W Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Bethesda, MD 20894, USA
Gene 443:12-21. 2009
..Second, a comparison of PfMsp-9 with the P. reichenowi ortholog indicated retention of a significant inter-unit diversity within an 18-base pair repeat within the coding region of P. falciparum, but homogenization in P. reichenowi...
- Intronization, de-intronization and intron sliding are rare in Cryptococcus
Scott W Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
BMC Evol Biol 9:192. 2009
..Two recent papers suggest that such changes may be a major force in remodeling of eukaryotic gene structures, however the rate of occurrence of such changes has not been assessed at the genomic level...
- Rates of intron loss and gain: implications for early eukaryotic evolution
Scott William Roy
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 102:5773-8. 2005
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- The origin of recent introns: transposons?
Scott W Roy
Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Genome Biol 5:251. 2004
..A recent study makes considerable progress by identifying numerous recently gained introns in nematodes - although it remains difficult to distinguish definitively between models of intron gain...
- Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis
Manuel Irimia
Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
Mol Biol Evol 25:375-82. 2008
..Finally, we demonstrate an inverse relationship between AS and gene duplication, suggesting that the latter may be primarily responsible for the emergence of new functional transcripts in nematodes...
- Quantitative regulation of alternative splicing in evolution and development
Manuel Irimia
Departament de Genetica, and Institut de Biomedicina IBUB, Universitat de Barcelona, Barcelona, Spain
Bioessays 31:40-50. 2009
..We discuss the potential role of changes in developmental regulation of AS as an additional layer in complex gene regulatory networks and in the emergence of genetic novelties...
- Mystery of intron gain: new data and new models
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
Trends Genet 25:67-73. 2009
..In addition, we introduce two potential mechanisms for intron creation, based on hybrid RNA-DNA reverse splicing and on template switching errors by reverse transcriptase...
- Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
PLoS Genet 4:e1000148. 2008
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- Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
PLoS ONE 4:e5800. 2009
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- Phylogenomics: gene duplication, unrecognized paralogy and outgroup choice
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS ONE 4:e4568. 2009
..Overall, these results generalize the utility of closely-related outgroups for phylogenetic analysis...
- The signal of ancient introns is obscured by intron density and homolog number
Scott William Roy
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 99:15513-7. 2002
..This finding matches the expectation of the mixed model of intron origin, in which a fraction of phase zero introns are left from the assembly of the first genes, while other introns have been added in the course of evolution...
- Probing evolutionary repeatability: neutral and double changes and the predictability of evolutionary adaptation
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS ONE 4:e4500. 2009
..5x10(-7)%) pathways were characterized by consistently increasing resistance, thus only a tiny fraction of possible paths are accessible by positive selection. I further explore these data in several ways...
- Patterns of polymorphism in genomic regions flanking three highly polymorphic surface antigens in Plasmodium falciparum
Olukemi K Amodu
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Mol Biochem Parasitol 159:1-6. 2008
..A higher ratio of SNPs to indels than previously reported for P. falciparum was observed. An 11 bp repeat upstream of msp2 showed an intriguing pattern of polymorphism possibly suggestive of purifying selection on total allele length...
- Recent evidence for the exon theory of genes
Scott William Roy
Genetica 118:251-66. 2003
..Thus, this moderated form of the Exon Theory of Genes still offers a coherent picture of the origin and evolutionary history of the intron-exon structure of eukaryotic genes...
- Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes
Scott William Roy
Mol Biol Evol 23:1824-7. 2006
..5 billion years. Nine other predicted introns are due to annotation errors reflecting apparent mistakes in the E. histolytica genome assembly. These results underscore the massive differences in intron gain rates through evolution...
- Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata
Manuel Irimia
Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
Mol Biol Evol 24:1604-7. 2007
..Including the additional species paints a very different picture, with 13 remaining characters consistent with Ecdysozoa versus only 1 consistent with Coelomata...
- Origin of introns by 'intronization' of exonic sequences
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
Trends Genet 24:378-81. 2008
..Intronization is more common than the reverse process, loss of splicing of retained introns. Finally, these findings link alternative splicing with modern intron creation...
- Spliceosomal introns as tools for genomic and evolutionary analysis
Manuel Irimia
Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
Nucleic Acids Res 36:1703-12. 2008
..We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions...
- Rare genomic characters do not support Coelomata: RGC_CAMs
Scott William Roy
J Mol Evol 66:308-15. 2008
..These results indicate that the Coelomata signal is a long-branch artifact...
