The WFDC locus in human and other primates. (A) The long-range organization of the WFDC locus on human chromosome 20q13 is depicted (oriented relative to the centromere [CEN] and telomere [TEL]) and consists of the two indicated subloci separated by a 215-kb region containing unrelated genes (gray rectangle). The 145-kb centromeric WFDC sublocus contains the indicated six genes and four pseudogenes. The 322-kb telomeric WFDC sublocus contains the indicated 10 genes and one pseudogene. (B) The long-range organization of the centromeric WFDC sublocus in human and 12 nonhuman primates is depicted, as deduced by comparative analyses of the orthologous genomic sequences (see Table 2). Also shown are the two genes immediately flanking this sublocus on each side. Solid arrows represent small serine protease inhibitor genes and trappin (WFDC and PI3, respectively); open arrows represent semenogelin genes (SEMG); hatched arrows represent nonrelated neighboring genes; gray arrows with an X represent WFDC, trappin, and SEMG pseudogenes. The direction of all arrows reflects the gene’s transcriptional orientation. //, Gap between sequenced BACs (clone gaps in Table 2). “St” under a gene indicates the presence of a premature stop codon; “Fs” under a gene indicates the presence of a frameshift; “D” under a gene indicates that the corresponding sequence was retrieved from public databases rather than generated as part of this study (specifically, for chimpanzee, macaque, and orangutan). Note that squirrel monkey has two SEMG1 genes, labeled as “1a” and “1b” below each, and that owl monkey has a single unique SEMG gene (a SEMG1-SEMG2 chimera, which is labeled below the gene with an *). The two boxed areas reflect the WFDC12-to-ΨPI3 and PI3-to-ΨWFCD15d paralogous duplicons, respectively. (C) The G + C content of the human centromeric WFDC sublocus is shown. The Y-axis is scaled to reflect a minimum of 43% and maximum of 70% G + C content. Note the alternating genomic segments of low (I and III) and high (II and IV) G + C content. Also shown are the positions of CpG islands (defined as >200-bp stretches of sequence with a G + C content of >50% and an observed CpG to expected CpG ratio of >0.6). Note that panel C is drawn to scale relative to panel B.

Relationships of semen coagulation, SEMG protein length, and mating system among primates. Primates are grouped according to their established mating system (Dixson 1997): monogamy, polygyny, dispersed, and multimale–multifemale. Semen coagulation is rated on a four-point scale (Dixson and Anderson 2002), with 1 reflecting no coagulation and 4 reflecting the production of a solid copulatory plug (ND, semen coagulation data not available). The indicated gray bars reflect the number of repetitive domains (each 60 amino acids in length) per SEMG protein, indicated for SEMG1 (left) and SEMG2 (right). Open bars represent predicted truncated proteins due to a premature stop codon or frameshift. SEMG genes that are deleted or nearly deleted are indicated by *DEL* before the species name. The hatched bar for galago SEMG2 indicates a ∼3-kb galago-specific inserted sequence encoding 77 additional domains (each 13 amino acids in length). The sequences for gibbon SEMG1 and SEMG2, cotton-top tamarin SEMG2, and spider monkey SEMG2 were obtained from the public databases (see Methods). Squirrel monkey has no SEMG2 gene, but contains two copies of a SEMG1 gene that may be the product of a gene-conversion event (yielding SEMG1a and SEMG1b, respectively).

Sequence conservation between paralogous segments in the centromeric WFDC sublocus. (A) A dot plot depicts sequence conservation between the two paralogous segments that reside within the human centromeric WFDC sublocus. The X- and Y-axes represent the PI3-to-ΨWFCD15d and WFDC12-to-ΨPI3 duplicons, respectively (boxed regions in Fig. 1B). A schematic representation of the exon-based gene structures and pseudogenes is shown for each, with the positions of exons along the X-axis highlighted in the dot plot. The four SEMG genomic blocks (Sgb) are boxed and labeled. Sgb1 is larger than previously described (Ulvsback et al. 1992) and is fragmented into three pieces, as determined by comparison with the lemur sequence. The two paralogous segments have significant coding and noncoding sequence conservation (highlighted by dashed circles, four of which are labeled 1–4 and detailed in B and C). (B) PipMaker plots of three paralogous regions highlighted in A. (Left column, panel 1) ΨPI3 resides within a genomic segment that is 79% similar to a 774-bp region of PI3, including exon 1; (left column, panel 2) there is considerable conservation between PI3 and WFDC12, including the proximal 1495 bp of the 5′region (58% identical), the first exon (79% identical at the nucleotide level; 10/22 residues identical at the amino acid level), and the first PI3 intron with WFDC12 exons 2 and 3 (55% identical); (center column, panels 4) the three human WFDC15 pseudogenes show >79% sequence identity with each other as well as lower but significant identity with a 1.2-kb segment of mouse Wfdc15a and Wfdc15b (right column). (C) PipMaker plots showing the sequence conservation among the four paralogous human SEMG genomic blocks (Sgb1 to Sgb4). In all cases, the reference sequence is Sgb1. Newly identified Sgb3 and Sgb4 are truncated blocks that have lost all SEMG-coding sequences. The Sgb1/Sgb3 plot corresponds to the highlighted region 3 in panel A. Panels A and C are not to scale.

Evolutionary history of the centromeric WFDC sublocus. The major duplication, deletion, rearrangement, and pseudogenization events involved in the evolution of the centromeric WFDC sublocus since the split of rodents and primates are schematically cataloged. In each case, the two paralogous duplicons (configured in a head-to-head fashion) within the sublocus are represented by two horizontal rectangles. Solid and open circles indicate functional genes and nonfunctional pseudogenes, respectively; black, red, and blue circles represent WFDC, trappin, and SEMG/Svs genes, respectively. Genes are labeled A through O, with the specific names provided in the key at the bottom. The blue squares depict the two SEMG1 genes in squirrel monkey, which are the result of a gene-conversion event. A blue triangle depicts the single SEMG gene in owl monkey (a SEMG1-SEMG2 chimera). The evolutionary history of each gene can be traced along the indicated lineages by the colored lines. Divergence times are provided on the right (MYA, million years ago), as indicated by Goodman et al. (1998); note that this evolutionary timeline is not drawn to scale.