Transposable elements and genome evolution

R. Ruggiero, Y. Bourgeois and S. Boissinot (2017). LINE insertion polymorphisms are abundant but at low frequencies across populations of Anolis carolinensis. Frontiers in Genetics 4: 44.

S. Boissinot and A. Sookdeo (2016). The evolution of LINE-1 in vertebrates.  Genome Biology and Evolution 8(12): 3485-3507.

M. Tollis and S. Boissinot (2013). Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). Genome Biology and Evolution 5(9): 1754-1768. pdf

A. Sookdeo, C. Hepp, M. McClure and S. Boissinot (2013). Revisiting the evolution of mouse LINE-1 in the genomic era. Mobile DNA 4(1): 3. pdf

E. Blass, M. Bell and S. Boissinot (2012). Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback. Genome Biology and Evolution 4: 687-702. pdf

M. Tollis and S. Boissinot (2012). The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes. Genome Dynamics Vol.7: Repetitive DNA: 68-91.  

K. Kusumi, R.J. Kulathinal, A. Abzhanov, S. Boissinot, N.G. Crawford, B.C. Faircloth, T.C. Glenn, J.B. Losos, D.B. Menke, T.J. Sanger, C. Schneider, J. Wade, J. Wilson-Rawls (2011). Developing a community-based genetic nomenclature and comparative analysis of the anole lizard. BMC Genomics 12: 554.  

M. Tollis and S. Boissinot (2011). The transposable element profile of the Anolis genome: how a lizard can provide insights into the evolution of vertebrate genome size and structure. Mobile Genetics Elements 1: 107-111.

J. Alfoldi, F. Di Palma, M. Grabherr,..S. Boissinot,..P. Novick… et al. [47 authors] (2011). The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals. Nature 477: 587-591.

P. Novick, J. Smith, M. Floumanhaft, D. Ray and S. Boissinot (2011). The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. Genome Biology and Evolution 3: 1-14. pdf

M. Song, R.M. Haralick, and S. Boissinot (2010). Efficient and exact maximum likelihood quantization of genomic features using dynamic programming. Int. J. Data mining and Bioinformatics 4(2): 123-141. 

P. Novick, J. Smith, D. Ray and S. Boissinot (2010). Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene 449: 85-94. pdf

P. Novick, H. Basta, M. Floumanhaft, M. McClure, and S. Boissinot (2009). The evolutionary dynamics of non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals. Mol. Biol. Evol. 26: 1811-1822. pdf

A.V. Furano and S. Boissinot (2008). Long Interspersed Nuclear Elements (LINEs): Evolution (version 2.0). In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester.

M. Song and S. Boissinot (2007). Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination. Gene 390 (1-2): 206-213. 

D.J. Witherspoon, E.E. Marchani, W.S. Watkins, C.T. Ostler, S.P. Wooding, B.A. Anders, J.D. Fowlkes, S. Boissinot, A.V. Furano, A.R. Rogers, M.A. Batzer and L.B. Jorde (2006). Analysis of human population genetic structure and diversity comparing polymorphic L1 (LINE-1) and Alu insertions. Human heredity 62 (1): 30-46.  

S. Boissinot, J. Davis, A. Entezam, D. Petrov and A.V. Furano (2006). Fitness cost of LINE-1 (L1) activity in humans. Proc. Natl. Acad. Sci. USA 103 (25): 9590-9594. pdf

T. Graham and S. Boissinot (2006). The genomic distribution of L1 elements: the role of insertion bias and natural selection. Journal of Biomedicine and Biotechnology 2006: 1-5.  

H. Khan, A. Smit and S. Boissinot (2006). The evolution of human LINE-1 retrotransposons since the origin of primates. Genome Research 16(1): 78-87. pdf

S. Boissinot and A.V. Furano (2005). The recent evolution of human L1 retrotransposons. Cytogenetics and Genome Research 110(1-4): 402-406.

S.L. Martin, W-LP Li, AV Furano and S. Boissinot (2005). The structure of mouse and human L1 elements reflect their insertion mechanism. Cytogenetics and Genome Research 110(1-4): 223-228.

S. Boissinot, Entezam A, Young L, Munson P, and Furano AV (2004). The insertional history of an active family of LINE-1 retrotransposons in humans. Genome Research 14: 1221-1231.

A.V. Furano, D. Duvernell and S. Boissinot (2004). L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends in Genetics 20(1): 9-14.

S. Boissinot, C. Roos and A.V. Furano (2004). Different rates of LINE-1 retrotransposons amplification and evolution in New World monkeys. J. Mol. Evol. 58: 122-130.

M. Song, S. Boissinot, R.M. Haralick, I.T. Phillips (2003). Estimating recombination rate distribution by optimal quantization. Proceedings of IEEE Computational Systems Bioinformatics Conference 2003: 403-406.

A.V. Furano and S. Boissinot (2002). Long Interspersed Nuclear Elements (LINEs): Evolution in the "Nature Encyclopedia of the human Genome", McMillan Publisher, Pp 746-752.

S. Boissinot and A.V. Furano (2001). Adaptive evolution in LINE-1 retrotransposons. Mol. Biol. Evol. 18(12): 2186-2194.

S. Boissinot, A. Entezam and A.V. Furano (2001). Selection against deleterious LINE-1-containing loci in the human lineage. Mol. Biol. Evol. 18: 926-935.

S. Boissinot, P. Chevret and A.V. Furano (2000). L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17(6): 915-928.  

D. Casane, S. Boissinot, B.H.-J. Chang, L. Shimmin and W.-H. Li (1997). Mutation pattern variation among regions of the primate genome. J. Mol. Evol. 45: 216-226.

Phylogeography and Phylogenetics

J.D. Manthey, M. Tollis, A.R. Lemmon, E. Moriarty Lemmon and S. Boissinot (2016). Diversification in wild populations of the model organism Anolis carolinensis: a genome-wide phylogeographic investigation. Ecology and Evolution 6(22): 8115-8125.

X. Freilich, J.D. Anadon, J. Bukala, O. Calderon, R. Chakraborty, Evolutionary Genetics – Class of 2013 and S. Boissinot (2016). Comparative phylogeography of Ethiopian anurans: impact of the Great Rift Valley and Pelistocene climate change. BMC Evolutionary Biology 16(1): 206.

S. Boissinot, L. Alvarez, J. Giraldo-Ramirez and M. Tollis (2014). Neutral nuclear variation in baboons (genus Papio) provides insights into their evolutionary and demographic histories. Am. J. of Physical Anthropology 155: 621-634.

X. Freilich, M. Tollis and S. Boissinot (2014). Hiding in the highlands: evolution of a frog species complex of the genus Ptychadena in the Ethiopian highlands. Molecular Phylogenetics and Evolution 71: 157-169. pdf

M. Tollis and S. Boissinot (2014). Genetic variation in the green anole lizard (Anolis carolinensis) reveals island refugia and a fragmented Florida during the quaternary. Genetica 142: 59-72.

M. Tollis, G. Ausubel, D. Ghmire and S. Boissinot (2012). Multi-locus Phylogeographic and Population Genetic Analysis of Anolis carolinensis: Historical Demography of a Genomic Model Species. PLoS ONE 7: e38474. pdf

S. Boissinot and P. Boursot (1997). Discordant phylogeographic patterns between the Y chromosome and mitochondrial DNA in the house mouse: selection on the Y chromosome?. Genetics 46: 1019-1034.

S. Boissinot, I. Ineich, L. Thaler and C.-P. Guillaume (1997). Hybrid origin and clonal diversity in the parthenogenetic gecko, Lepidodactylus lugubris (Reptilia: Lacertilia) in French Polynesia. J. of Herpetology, 31 (2): 295-298.

A. Orth, E. Lyapunova, A. Kandaurov, S. Boissinot, P. Boursot, N. Vorontsov and F. Bonhomme (1996). The polytypic species Mus musculus in Transcaucasia. C. R. Acad. Sci. Paris, Serie III, 319: 435-441.

C.P. Guillaume, I. Ineich and S. Boissinot (1994). Allozyme evidence for specific status of the two French Polynesian skink species in the genus Emoia ( Reptilia : Lacertilia). Copeia, 1994 (4): 548-556.

P. Geniez, M. Geniez, S. Boissinot, P.C. Beaubrun and J. Bons (1991). The Moroccan herpetofauna: new observations, 2 [in french]. Bull. Soc. Herp. Fr., 59 : 19-27. 

Evolution of resistance to viruses

I. Fish and S. Boissinot (2016). Functional evolution of the OAS1 viral sensor: insights from Old World primates. Infection, Genetics and Evolution 44: 341-350.

I. Fish and S. Boissinot (2015). Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in Old World primates. Immunogenetics 67(9): 487-499.

W. Ferguson, S. Dvora, R. Fikes, A.C. Stone, and S. Boissinot (2012). Long-term balancing selection at the anti-viral gene OAS1 maintains functionally different alleles in chimpanzees. Molecular Biology and Evolution. 29(4): 1093-1103.

W. Ferguson, S. Dvora, J. Gallo, A. Orth and S. Boissinot (2008). Long term balancing selection at the West Nile virus resistance gene, Oas1b, maintains trans-specific polymorphism in the house mouse. Mol. Biol. Evol. 25(8): 1609-1618.

Evolution of color vision in primates

W.-H. Li, S. Boissinot, Y. Tan,  S.-K. Shyue and D. Hewett-Emmett (2000). Evolutionary genetics of primate color vision: recent progress and potential limits to knowledge. Evol. Biol. 32: 151-178.

W.-H. Li, Y. Tan, S. Boissinot, S.-K. Shyue and D. Hewett-Emmett (2000). Genetic diversity of color vision in primates in "The Biology of Biodiversity" (ed. M. Kato), Springer Verlag, Tokyo, Pp. 259-274.

S. Boissinot, Y. Tan, S.-K. Shyue, H. Schneider, I. Sampaio, K. Neiswanger, D. Hewett-Emmett and W.-H. Li (1998). Origins and antiquity of X-linked triallelic color vision systems in New World monkeys. Proc. Natl. Acad. Sci. USA 95: 13749-13754.

S.-K. Shyue, S. Boissinot, H. Schneider, I. Sampaio, M.P. Schneider, C.R. Abee, L. Williams, D. Hewett-Emmett, H.G. Sperling, J.A. Cowing, K.S. Dulai, D.M. Hunt and W.-H. Li (1998). Molecular genetics of spectral tuning in New World monkey color vision. J. Mol. Evol. 46: 697-702.  

S. Boissinot, Y.-H. Zhou, D. Hunt, D. Hewett-Emmett and W.-H. Li (1997). Origin and molecular evolution of the X-linked duplicate color vision genes in howler monkeys. Zool. studies 36: 360-369.