Transposable elements and genome evolution

Bourgeois, Y., Ruggiero, R., Manthey, J., & Boissinot, S. (2018). Recent secondary contacts, background selection and variable recombination rates shape genomic diversity in the model species Anolis carolinensisbioRxiv, 352922. pdf

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. pdf

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

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, phylogenetics & taxonomy

Roman, I., Y. Bourgeois, J. Reyes-Velasco, O. P. Jensen, J. Waldman & S. Boissinot. (Accepted). Contrasted patterns of divergence and gene flow among five fish species in a Mongolian rift lake following glaciation. Biological Journal of the Linnean Society

Reyes‐Velasco, J., Manthey, J. D., Freilich, X., & Boissinot, S. (2018). Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia. Molecular ecology27(9), 2256-2270. pdf

Grünwald, C., J. Reyes-Velasco, H. Franz-Chávez, K. I. Morales-Flores, I. T. Ahumada-Carrillo, J. M. Jones, and S. Boissinot (2018). Six new species of Eleutherodactylus (Anura: Eleutherodactylidae: subgenus Syrrhophus) from Mexico, with a discussion of their systematic relationships and the validity of related species. Mesoamerican Herpetology. 5(1): 7-81.

Reyes-Velasco, J., Manthey, J. D., Bourgeois, Y., Freilich, X., & Boissinot, S. (2018). Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data. PloS one13(2), e0190440.

Manthey, J. D., Reyes-Velasco, J., Freilich, X., & Boissinot, S. (2017). Diversification in a biodiversity hotspot: genomic variation in the river frog Amietia nutti across the Ethiopian Highlands. Biological Journal of the Linnean Society122(4), 801-813.

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. pdf

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.