Evolution of the glycophorin gene family in the hominoid primates

Analysis of nucleotide sequences of the human glycophorin A (GPA) and glycophorin B (GPB) genes has indicated that the GPA gene most closely resembles the ancestral gene, whereas the GPB gene likely arose from the GPA gene by homologous recombination. To study the evolution of the glycophorin gene family in the hominoid primates, restricted DNA on Southern blots from man, pygmy chimpanzee, common chimpanzee, gorilla, orangutan, and gibbon was probed with cDNA fragments encoding the human GPA and GPB coding and 3-untranslated regions. This showed the presence in all of the hominoid primates of at least one GPA-like gene. In addition, at least one GPB-like gene was detected in man, both chimpanzee species, and gorilla, strongly suggesting that the event that produced the GPB gene occurred in the common ancestor of man-chimpanzee-gorilla. An unexpected finding in this study was the conservation ofEcoRI restriction sites relative to those of the other four enzymes used; the significance of this observation is unclear, but raises the question of nonrandomness ofEcoRI restriction sites in noncoding regions. Further analysis of the evolution of this multigene family, including nucleotide sequence analysis, will be useful in clarification of the evolutionary relationships of the hominoid primates, in correlation with the structure and function of the glycophorin molecules, and in assessment of the role of evolution in the autogenicity of glycophorin determinants.This work was supported in part by National Institutes of Health Grants AM33463 and CA33000.     

Molecular phylogeny and evolution of the human endogenous retrovirus HERV-W LTR family in hominoid primates

Long terminal repeats (LTRs) of human endogenous retrovirus (HERV) have contributed to the structural change or genetic variation of primate genome that are connected to speciation and evolution. Using genomic DNAs that were derived from hominoid primates (chimpanzee, gorilla, orangutan, and gibbon), we performed PCR amplification and identified thirty HERV-W LTR elements. These LTR elements showed a 82-98% sequence similarity with HERV-W LTR (AF072500). Specifically, additional sequences (GCCACCACCACTGTTT in the gorilla and TGCTGCTGACTCCCATCC in the gibbon) were noticed. Clone OR3 from the orangutan and clone GI2 from the gibbon showed a 100% sequence similarity, although they are different species. This indicates that both LTR elements were proliferated during the last 2 to 5 million years from the integration of the original LTR element. A phylogenetic tree that was obtained by the neighbor-joining method revealed a wide overlap of the LTR elements across species, suggesting that the HERV-W LTR family evolved independently during the hominoid evolution.     

Examination of hominid evolution by DNA sequence homology

Hominoid phylogeny was investigated in terms of unique DNA sequence homologies. In comparisons from the human standpoint the ΔTe₅₀ DNA values were Man 0, chimpanzee 0·7, gorilla 1·4, gibbon 2·7, orangutan 2·9, and African green monkey 5·7. In comparisons from the orangutan standpoint the ΔTe₅₀ DNA values were orangutan 0, chimpanzee 1·8, Man 1·9, gorilla 2·3, gibbon 2·4 and African green monkey 4·3. These results indicate that chimpanzee and gorilla are cladistically closer to Man than to orangutan and other primates, and that gorilla DNA may have diverged slightly more from the ancestral state than chimpanzee or human DNA. Comparisons from chimpanzee and gorilla DNA standpoints are needed to achieve a more definitive picture of hominoid phylogeny.     

Multiple restriction fragment length polymorphisms associated with the Vc determinant of the MN blood group-related chimpanzee V-A-B-D system

Twelve restriction fragment length polymorphisms (RFLPs) were detected in common chimpanzee using two restriction enzymes (HindIII andMspI) and four DNA probes to the coding regions of the human glycophorin A (GPA) and glycophorin B (GPB) genes and their 3-untranslated regions. Seven RFLPs correlated with red cell expression of the V^c determinant of the MN blood group-related V-A-B-D system and five RFLPs correlated with nonexpression of this antigen. Animals heterozygous for theV allele that encodes the V^c determinant had all 12 polymorphic restriction fragments and appeared to show reduced intensity of probe hybridization to these fragments, consistent with the presence of aV and a non-V allele. No RFLPs were detected withEcoRI,SstI, orBamHI, in spite of the relatively large segment of DNA (at least 20 kb) involved in the polymorphisms. The RFLPs were chimpanzee specific and were not found in man, gorilla, orangutan, or gibbon. Multiple RFLPs distinguishing primate species are rare and may be useful markers for molecular evolution.This work was supported in part by National Institutes of Health Grants AM 33463 and CA 33000.     

Evolution of DNA on Y-chromosome in hominoid primates as examined by PCR

Every species of non-human primates, especially those of hominoids, has a variety of reproductive structures and accompanying male traits, such as sexual dimorphism and relative size of testis to body weight, which may be at least partly triggered by DNA on the Y-chromosome. Recently, a panel of PCR (Polymerase Chain Reaction) primer sets were designed to amplify various DNA segments spread over the human Y-chromosome. We applied these primer sets for amplification of DNA segments on the Y-chromosome of hominoid species: chimpanzee, bonobo (Pygmy chimpanzee), gorilla, orangutan, whitehanded gibbon, agile gibbon, and Japanese monkey as an out group. The DNA segments including SRY, testis determining factor, and ZFX/ZFY could be amplified clearly in males of all species examined. These highly conserved genes may serve important biological functions. However, as the phylogenic distance from humans increased, some of the DNA segments could not be amplified. For example, DYZ1 (SY160) could be amplified only using human DNA as a template, and DYF60S1 (SY61), DYZ217 (SY126) and DYS233 (SY148) could be amplified only using human and African great ape DNA. It is interesting to note that locus DYS250 (SY17) could not be amplified in chimpanzee and bonobo but amplified in gorilla and orangutan. Locus DYS251 (SY18) was amplified in all species except the white-handed gibbon. These results indicate that a variety of evolutionary events including mutation, deletion, insertion, and rearrangement occurred in Y-chromosome DNA during primate evolution.     

Studies on human red-cell membrane glycophorin A and glycophorin B genes in glycophorin-deficient individuals.

1. Genomic DNA derived from individuals who lack glycophorin A (GPA), glycophorin B (GPB) or both of these proteins was subjected to Southern-blot analysis using GPA and GPB cDNA probes. 2. Bands on the Southern blots were assigned to the GPA gene, GPB gene or to a putative pseudogene. 3. Genomic DNA derived from an individual of the Mk phenotype was shown to have deletions in the GPA and GPB genes. The simplest model for the results obtained is that a single deletion spans the GPA and GPB genes in the individual studied.     

Primate genes for glycophorins carrying MN blood group antigens

Glycophorin A, B, and E genes were derived from a common ancestral gene and this gene family appeared during primate evolution, probably between orangutan and gorilla divergences. Based on the study of genomic structures of these human glycophorins and the genetic and immunological study of primate glycophorins, we hypothesize that chimpanzee and gorilla glycophorin B could possess a longer extracellular region and carry a stronger N blood group antigenicity compared with that of the human.     

人与大猩猩,黑猩猩和猩猩亲缘关系的探讨

有关人锆超科的系统发育仍然存在刍议。争论焦点在与大猩猩和黑猩猩哪 个关系更近一点。酪氨酸酶是黑色素合成中的关键酶,酪氨酶基因的突变将导致白化病。测定了人猿科中大猩猩,黑猩猩、猩猩和长臂锆产基因全部５个外显子的ＤＮＡ序列。     

Comparative immunochemical studies of primate hemoglobins

The antigenic properties of a number of chromatographically purified primate hemoglobins were compared to those of normal human hemoglobin using a sensitive radioimmunochemical procedure. The degree of inhibition of the antigen-antibody reaction with heterologous hemoglobins appeared to be related to the structural similarity of these proteins to the normal human hemoglobin immunogen. With the exception of the baboon hemoglobin, the antigenicity of the hemoglobins paralleled the phylogeny of the primates. The gorilla and chimpanzee hemoglobins were antigenically identical to normal human hemoglobin, whereas the gibbon and orangutan hemoglobins were substantially more variable. Of the Old World monkey hemoglobins examined, the baboon produced lower inhibition values, suggesting a greater degree of structural dissimilarity than other Cercopithecoidea hemoglobins, which is compatible with a greater rate of evolutionary change occurring in this protein. Using the known amino acid sequences of human and other primate hemoglobins, we have attempted to identify antigenic determinant areas of the proteins.     

Gorilla and orangutan c-myc nucleotide sequences: Inference on hominoid phylogeny

The nucleotide sequences of the gorilla and orangutan myc loci have been determined by the dideoxy nucleotide method. As previously observed in the human and chimpanzee sequences, an open reading frame (ORF) of 188 codons overlapping exon 1 could be deduced from the gorilla sequence. However, no such ORF appeared in the orangutan sequence.The two sequences were aligned with those of human and chimpanzee as hominoids and of gibbon and marmoset as outgroups of hominoids. The branching order in the evolution of primates was inferred from these data by different methods: maximum parsimony and neighborjoining.Our results support the view that the gorilla lineage branched off before the human and chimpanzee diverged and strengthen the hypothesis that chimpanzee and gorilla are more related to human than is orangutan. Correspondence to: F. Galibert     

Evolution of butyrylcholinesterase in higher primates: an immunochemical study

Serum butyrylcholinesterase (BuChE; EC 3.1.1.8) of man and the higher primates was tested enzymatically and immunochemically, with the aid of monoclonal antibodies (McAb) developed against the enzyme isolated from human blood. Enzyme activities showed great differences across species and among individuals, but all samples tested were dibucaine-sensitive. One McAb showed similar affinities for BuChE of each species, but another showed marked differences in affinity, preferring species in the order: man greater than chimpanzee = pygmy chimpanzee greater than gorilla much greater than orangutan greater than gibbon. We conclude that at least one epitope of BuChE underwent progressive modification during the later stages of primate evolution.     

Phylogenetic Analysis of a Retroposon Family in African Great Apes

The SINE-R retroposon family has been identified by its relationship with the long terminal repeats (LTRs) of human endogenous retrovirus class K (HERV-K) as a mobile element that has evolved recently in the human genome. Here we examined the recent evolutionary history of this class of elements by a PCR approach to genomic DNA from the African great apes and by phylogenetic analysis including comparison with the HERV K10 parent sequence. With primers derived from a cDNA sequence from human brain, we identified 27 sequences from the chimpanzee and 16 from the gorilla. Phylogenetic comparisons with previously recognized sequences from the human and from the orangutan and gibbon revealed wide overlap of elements across species, suggesting multiple origins in the course of hominoid evolution. Two human elements SINE-R.C2 and HS307 were the furthest removed from the HERV-K10 sequence but these two elements were closely related to three elements from the chimpanzee and four elements from the gorilla. This group of elements (our clusters 14 and 15) appears to have transposed late in hominoid evolution. One element (Ch-M16) showed 99.1% sequence identity with the SINE-R.C2 element, which is human-specific. Thus the SINE-R family appears to have continued to be active in transposition throughout the course of primate evolution. Received: 12 March 1999 / Accepted: 25 May 1999     

人猿超科和旧大陆猴7种高等灵长类FKN全基因序列的测定及进化分析

测定人猿超科(人、黑猩猩、大猩猩、红毛猩猩和长臂猿)和旧大陆猴(猕猴和叶猴)7种高等灵长类FKN全基因序列, 探讨其系统进化分析。用简并引物PCR(Degenerated PCR)法分别扩增FKN的3个外显子, 其产物经琼脂糖凝胶回收、纯化后测序, 然后用BioEdit软件剪切拼接FKN基因全序列, 用DNAStar比对后比较基因和氨基酸序列同源性, Mega软件重构FKN基因进化树, 应用Datamonkey分析FKN的负选择位点。序列分析发现人猿超科较旧大陆猴FKN基因除了有散在的点突变外, 还有一明显的30 bp的核苷酸缺失突变; 人FKN基因序列与黑猩猩、大猩猩、红毛猩猩、长臂猿、猕猴和叶猴的同源性分别是99.2%、98.4%、98.1%、96.5%、95.9%和93.8%, 由此推导的氨基酸序列同源性分别是98.5%、98.0%、97.7%、94.7%、93.7%和90.5%; FKN基因进化树表明人与黑猩猩关系更近, FKN基因进化和通常认为的物种进化一致; Datamonkey分析结果显示FKN存在3个负选择位点53Q、84D、239N。成功获得人、黑猩猩、大猩猩、红毛猩猩、长臂猿、猕猴和叶猴7种高等灵长类物种FKN全基因序列, 为后续探讨FKN在高等灵长类物种进化过程中免疫学功能演变及其结构与功能的关系奠定基础。     

Karyotype of the gibbons hylobates lar and h. moloch inversion in chromosome 7.

A karyotype of the gibbon, Hylobates, has been prepared based on the chromosome banding patterns produced by quinacrine, trypsin-Giemsa, and centromeric heterochromatin stains. The banding patterns of H. lar and H. moloch are virtually identical. No brilliant quinacrine-fluorescent areas are present. The banding pattern of most of the gibbon chromosomes show less resemblance to those of the human, chimpanzee, gorilla, or orangutan than the chromosomes of the higher primates do to each other, suggesting a relatively large evolutionary separation of the gibbon from the higher primates. A pericentric inversion of chromosome 7 is present in one gibbon.     

Sequence diversification and exon inactivation in the glycophorin A gene family from chimpanzee to human

In humans, the allelic diversity of MNSs glycophorins (GP) occurs mainly through the recombinational modulation of silent exons (pseudoexons) in duplicated genes. To address the origin of such a mechanism, structures of GPA, GPB, and GPE were determined in chimpanzee, the only higher primate known to have achieved a three-gene framework as in humans. Pairwise comparison of the chimpanzee and human genes revealed a high degree of sequence identity and similar exon-intron organization. However, the chimpanzee GPA gene lacks a completely formed M- or N-defining sequence as well as a consensus sequence for the Asn-linked glycosylation. In the case of the GPB gene, exon III is expressed in the chimpanzee but silenced, as a pseudoexon, in the human. Therefore, the protein product in the chimpanzee bears a larger extracellular domain than in the human. For the GPE genes, exon III and exon IV have been inactivated by identical donor splice-site mutations in the two species. Nevertheless, the chimpanzee GPE-like mRNA appeared to be transcribed from a GPB/E composite gene containing no 24-bp insertion sequence in exon V for the transmembrane domain. These results suggest a divergent processing of exonic units from chimpanzee to human in which the inactivation of GPB exon III preserved a limited sequence repertoire for diversification of human glycophorins.Correspondence to: O.O. Blumenfeld     

Serum cholinesterase activities and inhibition profiles of nonhuman primates

Serum cholinesterase activities and inhibition profiles of 169 chimpanzees, 15 gorillas, 26 orangutans, seven gibbons, and 12 rhesus monkeys were determined. Mean values of activities against benzoylcholine (μmols/min/ml) and dibucaine, fluoride, and Ro 2-0683 numbers (percentage inhibition of benzoylcholine hydrolysis) are: chimpanzee, 2.276, 80, 64, and 97; gorilla, 9.403, 82, 71, and 96; orangutan, 0.747, 94, 6, and 98; gibbon, 0.071, 89, 7, and 94; and rhesus monkey, 0.859, 95, 10, and 99, respectively. Sernylan numbers were determined of the last 100 chimpanzee serums collected and of each of the gorilla, orangutan, gibbon, and rhesus monkey serums. Mean values of Sernylan numbers are: chimpanzee, 80; gorilla, 81; orangutan, 95; gibbon, 94; and rhesus monkey, 96. The chimpanzee and the gorilla have dibucaine, fluoride, Ro 2-0683, and Sernylan numbers within the range found in men who are homozygotes for the usual cholinesterase (genotype E₁^uE₁^u). No cholinesterase variant was found in any chimpanzee or gorilla. The orangutan, gibbon, and rhesus monkey have inhibition profiles that resemble one another, with higher dibucaine and Sernylan numbers and much lower fluoride numbers than the chimpanzee or the gorilla. The results of the inhibition tests suggest that the African apes, chimpanzee and gorilla, are related more closely to man than are the Asian apes, orangutan and gibbon.     

Anti-human red cell monoclonal antibodies produced by macaque-mouse heterohybridomas: their reactivity with human and nonhuman primate erythrocytes.

Eighteen monoclonal antibodies (Mabs) against human red blood cells (RBCs) produced by macaque mouse heterobybridomas gave uniformly positive reactions with all human samples except for some with particular null phenotypes. Based on reactions with latter cells, the human antigenic targets of 11 antibodies could be identified: six were specific for glycophorin-related antigens (Wr(b), En(a), Ge4), and each of the live remaining antibodies showed one of the following specificities: CD55, CD44, CD59, Kell, and Rh proteins. Four Mabs recognized the Vc antigen of the chimpanzee V-A-B-D system. Six macaque Mabs detected polymorphisms in chimpanzee, gorilla, orangutan, and gibbon that did not correspond to any known blood group in these animals, while other Mabs gave monomorphic reactions with ape RBCs. The reagents produced by macaque hybridomas are useful tools not only for human blood grouping tests, but also for tracing the relationships among blood group antigens of man and anthropoid apes.     

Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes

Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrophoretic distances. They were applied to data for the human, chimpanzee, gorilla, orangutan, and gibbon species. Among the four different sets of data used, DNA sequences for an 895-nucleotide segment of mitochondrial DNA (Brown et al. 1982) gave the most reliable tree, whereas electrophoretic data (Bruce and Ayala 1979) gave the least reliable one. The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species. The orangutan and gibbon are more distantly related to man than is the gorilla. This topology of the tree is in agreement with that for the tree obtained from chromosomal studies and DNA-hybridization experiments. However, the difference between the branching point for the human and the chimpanzee species and that for the gorilla species and the human-chimpanzee group is not statistically significant. In addition to this analysis, various factors that affect the accuracy of an estimated tree are discussed.