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Ray, D. A, and M. A. Batzer (Submitted) Tracking Alu Evolution in New World

        Primates. BMC Evolutionary Biology.

Supplementary Data

McAliley. L.R., R.E. Willis, D.A. Ray, P.S. White and L.D. Densmore (Under revision)  

        Are crocodiles monophyletic?: DNA sequence evidence from nuclear and

mitochondrial coding genes and the mitochondrial control region. Molecular

Phylogenetics and Evolution.

Ray, D. A, D. J. Hedges, S. W. Herke, J. D. Fowlkes, E. W. Barnes, D. K. LaVie, L.

        M. Goodwin and M. A. Batzer (In press) Chompy: An infestation of MITE-like

repetitive elements in the crocodilian genome. GENE.

Supplementary Data

Wang J., L. Song, M.K. Gonder, S.A.Tishkoff, S. Azrak, D.A. Ray, M.A. Batzer

        and Ping Liang (In press) Whole genome computational comparative

genomics:  a fruitful approach for ascertaining Alu insertion polymorphisms.

        GENE.

Supplementary Data

Walker, J.A., D.A. Ray, J. Shewale, S.K. Sinha and M.A. Batzer. (In press) Mobile

       Elements: Novel Genetic Systems for Forensic Genomics. In: Forensic DNA

       Typing (V.W. Weedn and R.E. Gaensslen, eds). Marcel Dekker, Inc. New York.

Ray, D.A., J.A. Walker, A. Hall, B. Llewellyn, J Ballantyne, A.T. Christian, K.

Turtletaub and M.A. Batzer. (In press) Inference of Human Geographic

       Origins Using Alu Insertion Polymorphisms. Forensic Science International.

Corrected proof

       Supplementary Data: 1 -  Primer and amplification conditions, 2 - Genotype

information, 3 - Structure output, 4 - WGA results

Xing, J., H. Wang, K. Han, D.A. Ray, C.H. Huang, L.G. Chemnick, C.-B. Stewart, T.

Disotell, O.A. Ryder and M.A. Batzer (In press) A mobile element based

phylogeny of Old World monkeys. Molecular Phylogenetics and Evolution.

Supplementary Data: Supplemental Table Supplemental Alignments

Salem, A-H, D.A. Ray, D.J. Hedges, J. Jurka and M. A. Batzer (2005) Analysis of

the human Alu Ye lineage.  BMC Evolutionary Biology 5:18. pdf

Ho, H.J., D.A. Ray, A.H. Salem, J.S. Myers, and M.A. Batzer. (2005)

       Straightening Out the LINEs: LINE-1 Element Orthologous Loci. Genomics 

       85:201-207.  pdf

Otieno, A.C., A.B. Carter, D.J. Hedges, J.A. Walker, D.A. Ray, R.K. Garber, B.A.

Anders, N. Stoilova, M.E. Laborde, J.D. Fowlkes, C.H. Huang, B. Perodeau, 

and M.A. Batzer. (2004) Analysis of the Human Alu Ya-lineage. Journal of

        Molecular Biology 342: 109-118. pdf

Ray, D.A., J. Xing, D.J. Hedges, M.A. Hall, M.E. Laborde, B.A. Anders, B.R.

      White, N. Stoilova, J.D. Fowlkes, K.E. Landry, L.G. Chemnick, O.A. Ryder,

and M.A. Batzer. (2005) Alu Insertion Polymorphisms and Platyrrhine

Primate Phylogenetic Relationships. Molecular Phylogenetics and Evolution. 

35(1): 117-126.  pdf

Supplementary Data:  Locus and primer data, Alignments,

Ray, D.A., J.A. Dever, S.G. Platt, T.R. Rainwater, A.G. Finger, S.T. McMurry,

       M.A. Batzer, B. Barr, P.J. Stafford, J. McKnight and L.D. Densmore. 2004. Low

       Levels of Nucleotide Diversity in Crocodylus moreletii and Evidence of

       Hybridization with C. acutus. Conservation Genetics 5(4): 449-462. pdf

Salem, A-H, D.A. Ray, M. A. Batzer. (2005) Identity by Descent and DNA Sequence

       Variation of Human SINE and LINE Elements.  Cytogenetic and Genome

       Research 108: 63-72. pdf

       Supplementary Data: Tables  Alignments

Salem, A.-H.^*, D.A. Ray^*, J. Xing, P.A. Callinan, J.S. Myers, D.J. Hedges, R.K.

        Garber, D.J. Witherspoon, L.B. Jorde and M.A. Batzer. 2003. Alu Elements and

        Hominid Phylogenetics. Proc Natl Acad Sci U S A 100(22): 12787-12791. pdf

       Supplementary Data: AluYe_alignment Appendix_1 Appendix_II

*These authors contributed equally to this work.

Stafford, P.J., S.T. McMurry, T.R. Rainwater, D.A. Ray, L.D. Densmore and B.

Barr. 2003. Morelet's crocodile (Crocodylus moreletii) in the Macal River

watershed, Maya Mountains, Belize. Herp Bull 85: 15-23. pdf

Gonzalez, Z., D. A. Ray, L. R. McAliley, M. J. Gray, C. Perchellet, L. M. Smith and

        L. D. Densmore (2004) A Set of Polymorphic Microsatellite Markers for the Great

        Plains Toad, Bufo cognatus. Mol Ecol Notes 4(1): 9-10. pdf

Ray, D. A. and L. D. Densmore. 2003. Repetitive Sequences in the Crocodilian

       Mitochondrial Control Region: Poly-A Sequences and Heteroplasmic Tandem

       Repeats. Mol Biol Evol 20(6): 1006-1013. pdf

Ray, D. A. and L. D. Densmore. 2002. The Crocodilian Control Region: General

       Structure, Conserved Sequences and Evolutionary Implications. J Exp Zool (Mol

Devel Evol) 294 (4): 334-345. pdf

Densmore, L. D and D. A. Ray. 2002. Genetic Markers as Tools for Management of

        Captive Crocodilian Populations. In “Memoria Primer Seminario Taller:

Capacitacion y Actualizacion en el Manejo Sostenible de Cocodrilos en Panama”

        pp. 136-150 Asociacon Panamena de Manejadores y Especialistas de Crocodylia,

Panama, Republica de Panama. (English version: pp. 205-214.).

Ray, D. A., P. S. White, H. V. Duong, T. Cullen, and L. D. Densmore.  2001. High

        Levels of Variation in the African Dwarf Crocodile (Osteolaemus tetraspis) In:

        Crocodilian Biology and Evolution (G. Grigg, F. Seebacher and C. Franklin, eds).

        pp. 58-69. Surrey Beatty and Sons, Chipping Norton.

Rainwater, T.R., L.M. Nespoli, A.G. Finger, D.A. Ray, S.G. Platt, P.N. Smith, L.

        D. Densmore, K.W. Selcer and S.T. McMurry. (Submitted) Vitellogenin Induction

in Morelet's Crocodiles from Contaminated Habitats in Northerm Belize. Archives

of Environmental Contamination and Toxicology.

Revised: 09/08/05.