Immunoglobulin Genomics in the Guinea Pig Figure 17. The alignment of amino acid sequences of J and C genes from guinea pig IgL chains. A, Alignment of the deduced amino acid sequences of the three guinea pig Jk gene segments. B, Alignment of the amino acid sequences of the Ck proteins from human, mouse and rabbit. C, Alignment of the deduced amino acid sequences of the eleven guinea pig Jl gene segments. D, Alignment of the amino acid sequences of the Cl proteins from human, mouse and rabbit. 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. doi:10.1371/journal.pone.0039298.g017 the total VH genes (413 pseudogenes vs. 507 total genes). The high frequency of gene duplication in variable region generated multiple VH copies, many of which became pseudogenes due to genomic drift [68]. The VH pseudogenes are not truly nonfunc- tional in some species, for example, in rabbits, the pseudogenes usually are used to generate immunoglobulin diversity by gene conversion [67]. Guinea pig VH gene segments were also divided into three gene families (families 1, 2 and 3), which were orthologous to human VH families 4, 2 and 3, respectively. The guinea pig exhibited a multiple gene family group, as observed in dogs (three families) [69], humans (seven families) [70,71], horses (seven families) [32,72] and mice (sixteen families) [73], yet different from the single family group observed in sheep [57], rabbits [74], camels [75], swine [76] and cattle [72]. The guinea pig VH genes were also classified into different clans as in other mammalian species [50,52,67,72,74,77,78,79]. Some reports have revealed that representative VH genes belong to all three VH clans in the human, mouse, cat and dog [67,77]. This characteristic is different in cattle, horses and sheep [50,52,72,78,79], which have lost much of their ancestral repertoire, and the VH genes only belong to clan II. Pigs and rabbits only have clan III genes [74,77,79]. VH genes of guinea pig are distributed in clans II and III, and the majority of VH genes (family 3) are most closely related to human VH3 (clan III), which has been proposed as the ancestral VH gene family [78,80]. These features are also found in swine and rabbits [74,76]. The precise evolutionary relationship among mammalian lineages has not yet been resolved [81]. Results of the relevant study show that marsupials and monotremes were estimated to have separated from the common ancestor of present-day placental mammals more than 130 million years ago, while the major radiation of the placental mammals occurred approximately 70–120 million years ago [82,83,84,85,86]. Certain V gene families which descended from common ancestor genes are orthologues between nonplacental mammals and placental mam- mals. For example, platypus (Monotreme), dog and human share the same ancestral gene families (VH3 and VH4), While the American short-tailed opossum (Monodelphis domestica), swine, rabbit and human share ancestral VH3 family, and artiodactyl species share ancestral VH4 family. With an older evolutionary origin in present day mammals [86], platypus have two ancestral VH gene families, while other mammals share one or two ancestral VH gene families. These could be explained by an inactivation or loss of VH gene members in these species during evolution [25]. For new VH gene families in human or mouse, the divergence of VH genes probably occurred after speciation. The ratio of functional Vk and Vl is variable within mammalian species, with the germline Vk genes being more abundant than Vl genes in humans (40 Vk genes vs. 30 Vl genes) and mice (Vk genes vs. Vl genes over 95%) [87]. This is also the case for the guinea PLoS ONE | www.plosone.org 15 June 2012 | Volume 7 | Issue 6 | e39298