Description of seven new non-human primate MHC-B alleles.
Explore the source record for details and available documents.
Alleles↗
Biomedical subjects
J Martínez-Laso
Publications and source records attributed to J Martínez-Laso.
Generation of the B*41 group of alleles as indicated by intron sequences.
The generation of the B*41 alleles has been analysed using exon 1, intron 1, exon 2, intron 2 and exon 3 sequences. Results showed that B*4102 may have been generated as the first B*41 allele by a recombination mechanism between B*400102 and B*0801 or B*4201 involving intron 2. B*4101, B*4104 and B*4107 alleles could have been generated from B*4102 by a gene conversion event taking three different fragments from sequences belonging to intron 2/exon 3 of B*45, B*50 or B*49 alleles. B*4105 and B*4106 could be generated from B*4101 allele by point mutations, and B*4103 generation is unclear due to the lack of intron 2. The importance of introns in HLA-B allele polymorphism generation is stressed.
Alleles↗
Origin of Mayans according to HLA genes and the uniqueness of Amerindians.
The HLA allele frequency distribution of the Mayans from Guatemala was studied and compared with those of other First American Natives and worldwide populations (a total of 12,364 chromosomes and 6182 individuals from 60 different populations). The main conclusions were (1): the closest Amerindian group to Mayans is the Arhuacs, who were the first recorded Caribbean Islands' inhabitants (2). Mayans are not so close to Mesoamerican Zapotec, Mixe and Mixtec Amerindians, who genetically cluster together. Mixe had been related to Mayans only on linguistic bases (3). DRB1*0407 and DRB1*0802 alleles are found in 50% of Mayans; these alleles are also found in other Amerindians, but the Mayans' high frequencies may be showing a founder effect for this Mesoamerican-Caribbean population (4). Extended Mayan specific HLA haplotypes are described for the first time (5). Language and genes do not completely correlate in microgeographical studies (6). Significant genetic input from outside is not noticed in Meso and South American Amerindians according to the genetic analyses; while all world populations (including Africans, Europeans, Asians, Australians, Polynesians, North American Na-Dene Indians and Eskimos) are genetically related. Meso and South American Amerindians tend to remain isolated in the neighbour joining analyses.
Alleles↗
The Old World sparrows (genus Passer) phylogeography and their relative abundance of nuclear mtDNA pseudogenes.
The phylogenetic relationships of genus Passer (Old World sparrows) have been studied with species covering their complete world living range. Mitochondrial (mt) cyt b genes and pseudogenes have been analyzed, the latter being strikingly abundant in genus Passer compared with other studied songbirds. The significance of these Passer pseudogenes is presently unclear. The mechanisms by which mt cyt b genes become pseudogenes after nuclear translocation are discussed together with their mode of evolution, i.e., transition/transversion mitochondrial ratio is decreased in the nucleus, as is the constraint for variability at the three codon positions. However, the skewed base composition according to codon position (in 1st position the percentage is very similar for the four bases, in 2nd position there are fewer percentage of A and G and more percentage of T, and in 3rd codon position fewer percentage of G and T and is very rich in A and C) is maintained in the translocated nuclear pseudogenes. Different nuclear internal mechanisms and/or selective pressures must exist for explaining this nuclear/mitochondrial differential DNA base evolutive variability. Also, the phylogenetic usefulness of pseudogenes for defining relationships between closely related lineages is stressed. The analyses suggest that the primitive genus Passer species comes from Africa, the Cape sparrow being the oldest: P. hispaniolensis italiae is more likely conspecific to P. domesticus than to P. hispaniolensis. Also, Passer species are not included within weavers or Estrildinae or Emberizinae, as previously suggested. European and American Emberizinae sparrows are closely related to each other and seem to be the earliest species that radiated among the studied songbirds (all in the Miocene Epoch).
Cell Nucleus↗
Polymorphism and distribution of HLA-DR2 alleles in Mexican populations.
DRB1*15/16 nucleotide polymorphism was analyzed in 68 DR2 positive individuals (18 Mexican Mestizos, 30 Mazatecans and 20 Nahuas), carrying a total of 75 DR2 haplotypes. HLA-DR2 was one of the most frequent specificities detected in Mazatecans and Nahuas with gene frequency (gf) of 0.232 and 0.141, respectively. In these populations DRB1*16 was the most frequent DR2 split (gf = 0.183 in Mazatecans and gf = 0.135 in Nahuas), whereas in Mexican Mestizos the most frequent was DRB1*15 (gf = 0.065). Four DRB1-DQB1 combinations in Mexican Mestizos, two in Mazatecans and one in Nahuas were in linkage disequilibrium. In spite of the restricted polymorphism, there were differences on DRB1*15/16 alleles found in Mexicans. DRB1*1501 a Caucasian allele was predominant in Mexican Mestizos, whereas DRB1*1602 an Amerindian allele was characteristic on Indian populations. An important difference was detected among the Amerindian populations studied since DRB1*1502 was only present in Mazatecans. This data corroborates the restricted polymorphism of DRB1*15/16 and the high frequency of DRB1*16 subtype in autochthonous American populations and suggest that the differences in gene frequencies of DRB1*15/16 alleles could be helpful in distinguishing each of these population.
Alleles↗
The origin of Palestinians and their genetic relatedness with other Mediterranean populations.
The genetic profile of Palestinians has, for the first time, been studied by using human leukocyte antigen (HLA) gene variability and haplotypes. The comparison with other Mediterranean populations by using neighbor-joining dendrograms and correspondence analyses reveal that Palestinians are genetically very close to Jews and other Middle East populations, including Turks (Anatolians), Lebanese, Egyptians, Armenians, and Iranians. Archaeologic and genetic data support that both Jews and Palestinians came from the ancient Canaanites, who extensively mixed with Egyptians, Mesopotamian, and Anatolian peoples in ancient times. Thus, Palestinian-Jewish rivalry is based in cultural and religious, but not in genetic, differences. The relatively close relatedness of both Jews and Palestinians to western Mediterranean populations reflects the continuous circum-Mediterranean cultural and gene flow that have occurred in prehistoric and historic times. This flow overtly contradicts the demic diffusion model of western Mediterranean populations substitution by agriculturalists coming from the Middle East in the Mesolithic-Neolithic transition.
Alleles↗
HLA genes in Macedonians and the sub-Saharan origin of the Greeks.
HLA alleles have been determined in individuals from the Republic of Macedonia by DNA typing and sequencing. HLA-A, -B, -DR, -DQ allele frequencies and extended haplotypes have been for the first time determined and the results compared to those of other Mediterraneans, particularly with their neighbouring Greeks. Genetic distances, neighbor-joining dendrograms and correspondence analysis have been performed. The following conclusions have been reached: 1) Macedonians belong to the "older" Mediterranean substratum, like Iberians (including Basques), North Africans, Italians, French, Cretans, Jews, Lebanese, Turks (Anatolians), Armenians and Iranians, 2) Macedonians are not related with geographically close Greeks, who do not belong to the "older" Mediterranenan substratum, 3) Greeks are found to have a substantial relatedness to sub-Saharan (Ethiopian) people, which separate them from other Mediterranean groups. Both Greeks and Ethiopians share quasi-specific DRB1 alleles, such as *0305, *0307, *0411, *0413, *0416, *0417, *0420, *1110, *1112, *1304 and *1310. Genetic distances are closer between Greeks and Ethiopian/sub-Saharan groups than to any other Mediterranean group and finally Greeks cluster with Ethiopians/sub-Saharans in both neighbour joining dendrograms and correspondence analyses. The time period when these relationships might have occurred was ancient but uncertain and might be related to the displacement of Egyptian-Ethiopian people living in pharaonic Egypt.
Africa, Northern↗
A novel HLA-A*6816 allele possible generated by a point mutation in a Chilean from Punta Arenas (Magellan Strait).
Explore the source record for details and available documents.
Alleles↗
Evolution of MHC-G in humans and primates based on three new 3'UT polymorphisms.
MHC-G is a class Ib (non-classical) major histocompatibility complex (MHC) whose functional and evolutionary characteristics are still under scrutiny. The study of noncoding sequences in the MHC genes may provide important phylogenetic information. In this work we have sequenced the MHC-G exon 8, which encodes for the 3'UT region, in different species of primates. It has been shown that: (1) a previously described 14 base pair (bp) deletion polymorphism is human-specific and the HLA-G alleles may be classified according to its absence or presence; (2) another newly described 3 bp deletion/insertion polymorphism is also human-specific; and (3) another newly described 51 bp deletion polymorphism is common to Pongidae and humans, but is not found in other primates belonging to the Cercopithecinae family. A hypothesis on the evolutionary pathway of this gene is put forward in the light of these findings.
3' Untranslated Regions↗
HLA-DR4 allele frequencies on Indian and Mestizo population from Mexico.
Using PCR-SSOP and sequencing, we examined DRB1*04 nucleotide polymorphism in 137 DR4-positive Mexican healthy individuals (46 Mexican Mestizos, 64 Mazatecans, and 27 Nahuas), carrying a total of 147 DR4 haplotypes. Eleven different DRB1*04 alleles were detected in Mexican Mestizo population, whereas, in the two Indian groups a restricted polymorphism was observed (5 variants in Mazatecans and 4 in Nahuas). DRB1*0407 was the most frequent allele (gf = 0.106 in Mexican Mestizos, gf = 0.281 in Mazatecans, and gf = 0.189 in Nahuas). In spite of the restriction in polymorphism, there were differences on DRB1*04 alleles found in Mexicans mainly between Mazatecan and Nahua populations. DRB1*0403 was characteristic allele in Nahua ethnic group, whereas, 0404 and 0411 were predominant alleles in Mazatecans. This data corroborates the restricted polymorphism of DRB1*04 alleles in American populations. In spite of the restriction in this polymorphism, differences in frequencies of DRB1*04 alleles could help distinguish each population.
Gene Frequency↗
HLA genes in Arabic-speaking Moroccans: close relatedness to Berbers and Iberians.
The gene profile of Arabic-speaking Moroccans has been compared with those of other Mediterranean populations in order to provide additional information about the history of their origins. Our HLA data suggest that most Moroccans are of a Berber (Imazighen) origin and that Arabs who invaded North Africa and Spain in the 7th century A.D. did not substantially contributed to the gene pool; however, they imposed their advanced culture and their religion. Present-day Egyptians are also related to Moroccan Berbers and this supports an ancient Saharan origin for part of the present-day Mediterraneans, particularly for the Arabic-speaking ones (also Algerians) and also for the older substratum of Mediterranean people.
Alleles↗
Lack of association between the polymorphism at the heat-shock protein (HSP70-2) gene and systemic lupus erythematosus (SLE) in the Mexican mestizo population.
Major histocompatibility complex (MHC) alleles have been recognized as genetic factors for developing systemic lupus erythematosus (SLE). In the present study we analyzed whether a heat-shock protein gene (HSP70-2) is involved in determining susceptibility to develop SLE in a Mexican Mestizo population. A HSP70-2 Pst I polymorphism was detected by a restriction fragment length polymorphism analysis of polymerase chain reaction (PCR-RFLP) in 107 SLE patients and 158 healthy controls. No statistically significant differences were observed in the HSP70-2 allele distribution between patients and healthy controls. HLA-DR analysis showed an increased frequency of HLA-DR3 allele in the patients group (P < 0.05, OR = 2.26, EF = 6.0%). On the other hand, when we analyzed HSP70-2 polymorphism in relation to HLA-DR3 allele, we could only detect an increased frequency of AB genotype in the DR3 negative patients (pC < 0.05, RR = 2.6, EF = 11.3%). Linkage disequilibrium was observed for three haplotypes: HLA-DR3-HSP70-2A (D = 0.03, D' = 0.67, P < 0.01); HLA-DR1-HSP70-2A (D = 0.03, D' = 0.86, P < 0.01) and HLA-DR8-HSP70-2B (D = 0.02, D' = 0.46, P = 0.02). Our data indicate that HSP70-2 gene polymorphism as opposed to the other ethnic groups does not appear to be relevant in SLE susceptibility in Mexican patients and that the distribution of the different alleles depend on the frequency of HLA alleles associated with them.
Alleles↗
The origin of Cretan populations as determined by characterization of HLA alleles.
The Cretan HLA gene profile has been compared with those of other Mediterranean populations in order to provide additional information regarding the history of their origins. The allele frequencies, genetic distances between populations, relatedness dendrograms and correspondence analyses were calculated. Our results indicate that the Indoeuropean Greeks may be considered as a Mediterranean population of a more recent origin (after 2000 B.C.), while all other studied Mediterraneans (including Cretans) belong to an older substratum which was present in the area since pre-Neolithic times. A significant Turkish gene flow has not been detected in the Greek or Cretan populations, although Greeks and Turks have two high frequency HLA-DRB-DQB haplotypes in common. It is proposed that Imazighen (Caucasoid Berbers living at present in the North African coast and Saharan areas) are the remains of pre-Neolithic Saharan populations which could emigrate northwards between about 8000-6000 B.C., when desert desiccation began. They also could be part of the stock that gave rise to Sumerians, Cretans and Iberians; this is supported by both linguistic and HLA genetic data.
Alleles↗
Iberia: population genetics, anthropology, and linguistics.
Basques, Portuguese, Spaniards, and Algerians have been studied for HLA and mitochondrial DNA markers, and the data analysis suggests that pre-Neolithic gene flow into Iberia came from ancient white North Africans (Hamites). The Basque language has also been used to translate the Iberian-Tartesian language and also Etruscan and Minoan Linear A. Physical anthropometry of Iberian Mesolithic and Neolithic skeletons does not support the demic replacement in Iberia of preexisting Mesolithic people by Neolithic people bearing new farming technologies from Europe and the Middle East. Also, the presence of cardial impressed pottery in western Mediterranean Europe and across the Maghreb (North Africa) coasts at the beginning of the Neolithic provides good evidence of pre-Neolithic circum-Mediterranean contacts by sea. In addition, pre-dynastic Egyptian El-Badari culture (4,500 years ago) is similar to southern Iberian Neolithic settlements with regard to pottery and animal domestication. Taking the genetic, linguistic, anthropological, and archeological evidence together with the documented Saharan area desiccation starting about 10,000 years ago, we believe that it is possible that a genetic and cultural pre-Neolithic flow coming from southern Mediterranean coasts existed toward northern Mediterranean areas, including at least Iberia and some Mediterranean islands. This model would substitute for the demic diffusion model put forward to explain Neolithic innovations in Western Europe.
Anthropology↗
Phylogeny and rapid northern and southern hemisphere speciation of goldfinches during the Miocene and Pliocene epochs.
Mitochondrial cytochrome b (cyt b) from 25 out of 31 extant goldfinches, siskins, greenfinches and redpolls (genus Carduelis) has been sequenced from living samples taken around the world, specimens have also been photographed. Phylogenetic analysis consistently gave the same groups of birds, and this grouping was generally related to geographical proximity. It has been supposed that Pleistocene glaciations played a crucial role in the origin of extant diversity and distribution of Northern Hemisphere vertebrates. Molecular comparison of most extant songbird species belonging to the genus Carduelis does not support this assertion. The fossil record of chicken and pheasant divergence time has been used to calibrate the molecular clock; cyt b DNA dendrograms suggest that speciation in Carduelinae birds occurred during the Miocene and Pliocene Epochs (9-2 million years ago) in both the Northern and Southern Hemispheres. Only about 4% average amount of nucleotide substitution per lineage is found between the most distant Carduelis species; this suggests a remarkably rapid radiation when compared with the radiation of other passerine songbird genera. In addition, a continuum of small songbird speciation may be found during the Miocene Epoch in parallel with speciation of other orders (i.e. Galliformes, chicken/pheasant). Pleistocene glaciations may have been important in subspeciation (i.e. Eastern European grey-headed goldfinches/Western European black-headed goldfinches) and also in ice-induced vicariance (isolation) (i.e. siskin in Western Europe vs. siskin in Far East Asia) around the world. European isolated Serinus citrinella (citril finch) is not a canary, but a true goldfinch. South American siskins have quickly radiated in the last 4 million years coinciding with the emergence of the Isthmus of Panama; probably, a North American siskin related to C. notata invaded a suitable and varied biotope (the South American island) for Carduelis birds. North American goldfinches may be renamed as siskins, because they have a distant genetic relationship with European goldfinches. Genus Acanthis could be dropped, and thus redpolls should be separated from twite and linnet, the latter (Europeans) probably being related to American goldfinches. Also, reproductive barriers are observed between closely related species and not between other more distant ones. Finally, a tentative classification for genus Carduelis species is suggested.
Animals↗
Description of a new kind of MHC DNA sequence in Saguinus oedipus (cotton-top tamarin).
The MHC class I genes of the New World primate the cotton-top tamarin (Saguinus oedipus) are an exception to the high polymorphism and variability usually displayed by this multigene family. In the present work, the cloning and sequencing of a new pseudogene, tentatively named Saoe-Mhc-N4, in this primate species are reported. This new sequence has two characteristic deletions at exon 2, making it very unlikely that any putative protein from this sequence was an antigen-presenting molecule. Comparison of intron 1, intron 2, partial exon 1, exon 2 and partial exon 3 showed little similarity with those of classical class I genes and pseudogenes in S. oedipus and in other primates. Phylogenetic analysis grouped this Saoe-Mhc-N4 sequence with other pseudogenes in S. oedipus. Thus, it seems that Saoe-Mhc-N4 is an inactivated gene or a pseudogene which has been originated by the common process of duplication and subsequent inactivation of MHC class I loci in this primate species.
Alleles↗
Complete cDNA sequence of the HLA-DRB1*09012 allele.
Sequencing studies of HLA class II molecules have focused almost exclusively on exon 2. In this study the complete cDNA sequence of the DRB1*09012 allele is reported for the first time. This sequence was previously only partially published. In the DR9 antigen, two synonymous allelic variants (DRB1*09011 and 09012) were officially recognized, though it was later found that the first one contained an error and both sequences were, thus, identical.
Alleles↗
Description of two Mhc-C-related sequences in the New World monkey Saguinus oedipus.
Two new Mhc class I partial exon 1, intron 1, exon 2, intron 2 and partial exon 3 DNA sequences from the New World monkey Saguinus oedipus (Saoe) are described. These two sequences show certain Mhc-C sequence-specific changes. The only difference between these two new sequences is a productive substitution at position 152 [GCG (Ala)-->GAG (Glu)]. This change occurs in a position which in Mhc classical class I molecules affects the interaction between the peptide and the T-cell receptor. A dendrogram with Mhc sequences from different loci and different species was constructed, which clearly shows that these two new sequences cluster closer to Mhc-C sequences than to others. These data suggest that the new sequences may be related to the Mhc-C locus, and they have been named Mhc-Saoe-CR*01 and -CR*02. However, they share only a few of the conserved residues (from gorilla to human) of Mhc-C sequences, which suggests that the relationships with an ancestor of the Mhc-C lineage are very distant or that these two sequences are products of convergent evolution to perform a C locus related function. Furthermore, in the fragment of DNA sequenced, there is a loss of two invariant residues conserved in antigen-presenting molecules from reptiles to humans; thus, it is unlikely that these two Mhc-C-like sequences have an antigen-presenting function, or even that they are two alleles of a pseudogene; however, the G + C percentage (86.1%) at the third base of codons approaches that of an expressed gene in Saoe. It is concluded that Mhc molecules with C-locus characteristics existed in primates 50 million years ago and that this does not support a more recent origin of Mhc-C genes.
Alleles↗