Supporting Information Figure S1 Alignment of IgM amino acid sequences from several vertebrate species. Elephant IgM was compared with a panel of vertebrate IgM sequences. Dots indicate similar residues as in elephant m, whereas dashes indicate gaps introduced for optimal alignment. The cysteine residues C and W important for intra-domain disulfide bonds are shown on the first line of the alignment. (TIF) Figure S2 Alignment of the elephant IgD remnant with the IgD CH3 domains of several mammalian species. Amino acid residues that are identical to the top counterpart in every panel are shown as dots; Gaps and missing data are indicated by hyphens. Stop codons are indicated by stars. (TIF) Figure S3 Phylogenetic tree of the immunoglobulin gamma heavy chains of some mammalian species. The phylogenetic tree was constructed from the amino acid sequences of the CH3 exons of the immunoglobulin gamma heavy chains of various mammalian species. The credibility value for each node is shown. (TIF) Figure S4 87 Elephant germline DH segments. The nonamers (9-mer) and heptamers (7-mer) are displayed. Heptamer components that are different from the consensus (59: CACTGTG and 39: CACAGTG) are shadowed. The deduced amino acids of all three reading frames of the coding region of D segments are shown. Except DH, which has a 10 bp spacer, all the DH segments were attached by 12 bp spacer. (TIF) References 1. Thomas MG, Hagelberg E, Jone HB, Yang Z, Lister AM (2000) Molecular and morphological evidence on the phylogeny of the Elephantidae. Proc Biol Sci 267: 2493–2500. 2. Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, et al. (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409: 614–618. 3. Mikota SK, Peddie L, Peddie J, Isaza R, Dunker F, et al. (2001) Epidemiology and diagnosis of Mycobacterium tuberculosis in captive Asian elephants (Elephas maximus). J Zoo Wildl Med 32: 1–16. 4. Lyashchenko KP, Greenwald R, Esfandiari J, Olsen JH, Ball R, et al. 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Analysis of the Elephant Immunoglobulin Genes Figure S5 The alignment of amino acid sequences of J and C genes from elephant IgL chains. A, alignment of the deduced amino acid sequences of the three elephant Jk gene segments. B, alignment of the amino acid sequences of the Ck proteins from several mammalian species. C, alignment of the deduced amino acid sequences of the two elephant Jl gene segments. D, alignment of the deduced amino acid sequences of three elephant Cl genes and several mammalian species Cl genes. Amino acid residues that are identical to the top counterpart in every panel are shown as dots; Gaps and missing data are indicated by hyphens. (TIF) Table S1 The elephant immunoglobulin heavy chain and light chain DNA segments located in scaffolds 57, 202, 50, 86, and 68. (RAR) Table S2 GenBank accession numbers or references of the gene sequences from other species used in this paper. (RAR) Table S3 The eight elephant Vk gene families from scaffolds 202, 50, and 86. 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