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R Barrantes

Publications and source records attributed to R Barrantes.

At least 19 recordsLinked to original sources
PubMed2007

Molecular variability of the 16p13.3 region in Amerindians and its anthropological significance.

A total of 1558 base pairs in the 16p13.3 region were investigated in 98 individuals of Mongolian, Northern Arctic and Amerindian affiliation, and the results compared with those obtained in a previous worldwide study of the same genomic region. Fifty-five polymorphic sites could be classified into thirty-five haplotypes from the total data. A median joining network based on the haplotypes revealed two distinct clusters: one with low diversity, with haplotypes found in all five geographic-ethnic categories; while the other, with the most divergent haplotypes, was composed mainly of Africans and a few Amerindians. Almost all neutrality parameters yielded significantly negative values. Demographic simulations with the exclusively Amerindian dataset rejected all scenarios, including a bottleneck beginning more than 12,000 years ago. The demographic scenarios tested considering population growth were similar among the Amerindian and worldwide or Eurasian data sets. The results suggest that Amerindians are a representative sample of Eurasian populations, preserving the signal of demographic growth from the out of Africa exodus and, together with data from uniparental markers, support a scenario of a bottleneck of moderate intensity during the peopling of the New World.

American Indian or Alaska Native↗
PubMed2004

Intra- and intercontinental molecular variability of an Alu insertion in the 3' untranslated region of the LDLR gene.

One-hundred three individuals from two Mongolian, two Siberian, and ten native American populations were studied in relation to a 340-bp sequence from an Alu insertion located in the 3' untranslated region of the LDLR gene. Seven haplotypes have been determined, and haplotype B1 was the most common, accounting for about half the sequences found. In general, diversity values are quite high, about 2.5 times higher than those found in other autosomal Alu sequences. Almost all (93%) of the variability occurs at the intrapopulation level, but the greatest among-group differentiation (6-8%) was found when we grouped in a single population all Native Americans plus Siberian Eskimos and Chukchi and compared them with Mongolians. This result is compatible with earlier mtDNA and Y-chromosome suggestions of a single origin for the first colonizers of the American continent. With this nuclear locus it was not possible to broadly distinguish between Central and South American natives. No evidence of selection or marked demographic changes was obtained with these data.

3' Untranslated Regions↗
PubMed2003

Gene admixture in the Costa Rican population.

The general population of Costa Rica has sometimes been considered to be the product of an amalgamation of groups of diverse origin. To determine the magnitude of accumulated admixture since Spanish colonization, 11 classic genetic markers were analyzed in a total of 2196 individuals originating from five distinct regions of the country. A maximum likelihood approach was used. The proportions of genes of European, Amerindian and African ancestry were found to be 61%, 30% and 9% of the total population, respectively. Variation was observed at a regional level, with an increased European influence in the North (66%) and Central (65%) regions. Meanwhile an increase in Amerindian ancestry was found in the South (38%), and a higher incidence in the contribution of African genes was detected in the coastal regions (13% in the Atlantic and 14% in the North Pacific). A principal component (PC) analysis showed that 76% of the existing variability can be explained by the first two PCs, which is in agreement with the variations observed in the admixture process by geographic area. It has been concluded that the Costa Rican population is truly trihybrid, similar to populations in other Latin American countries; however, it differs from them fundamentally by the proportion of gene flow from ancestral populations.

Blood Group Antigens↗
PubMed2000

A second locus for an axonal form of autosomal recessive Charcot-Marie-Tooth disease maps to chromosome 19q13.3.

Autosomal recessive Charcot-Marie-Tooth disease (CMT) represents a heterogeneous group of disorders affecting the peripheral nervous system. The axonal form of the disease is designated as "CMT type 2" (CMT2), and one locus (1q21.2-q21.3) has been reported for the autosomal recessive form. Here we report the results of a genomewide search in an inbred Costa Rican family (CR-1) affected with autosomal recessive CMT2. By analyzing three branches of the family we detected linkage to the 19q13.3 region, and subsequent homozygosity mapping defined shared haplotypes between markers D19S902 and D19S907 in a 5.5-cM range. A maximum two-point LOD score of 9.08 was obtained for marker D19S867, at a recombination fraction of.00, which strongly supports linkage to this locus. The epithelial membrane protein 3 gene, encoding a PMP22 homologous protein and located on 19q13.3, was ruled out as being responsible for this form of CMT. The age at onset of chronic symmetric sensory-motor polyneuropathy was 28-42 years (mean 33.8 years); the electrophysiological data clearly reflect an axonal degenerative process. The phenotype and locus are different from those of demyelinating CMT4F, recently mapped to 19q13.1-13.3; hence, the disease affecting the Costa Rican family constitutes an axonal, autosomal recessive CMT subtype (ARCMT2B).

Adult↗
PubMed1996

Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations.

We have analyzed five microsatellite loci from the nonrecombining portion of the human Y chromosome in 15 diverse human populations to evaluate their usefulness in the reconstruction of human evolution and early male migrations. The results show that, in general, most populations have the same set of the most frequent alleles at these loci. Hypothetical ancestral haplotypes, reconstructed on the basis of these alleles and their close derivatives, are shared by multiple populations across racial and geographical boundaries. A network of the observed haplotypes is characterized by a lack of clustering of geographically proximal populations. In spite of this, few distinct clusters of closely related populations emerged in the network, which are associated with population-specific alleles. A tree based on allele frequencies also shows similar results. Lack of haplotypic structure associated with the presumed ancestral haplotypes consisting of individuals from almost all populations indicate a recent common ancestry and/or extensive male migration during human evolutionary history. The convergent nature of microsatellite mutation confounds population relationships. Optimum resolution of Y chromosome evolution will require the use of additional microsatellite loci and diallelic genetic markers with lower mutation rates.

Alleles↗
PubMed1996

Distribution and evolution of CTG repeats at the myotonin protein kinase gene in human populations.

We have analyzed the CTG repeat length and the neighboring Alu insertion/deletion (+/-) polymorphism in DNA samples from 16 ethnically and geographically diverse human populations to understand the evolutionary dynamics of the myotonic dystrophy-associated CTG repeat. Our results show that the CTG repeat length is variable in human populations. Although the (CTG)5 repeat is the most common allele in the majority of populations, this allele is absent among Costa Ricans and New Guinea highlanders. We have detected a (CTG)4 repeat allele, the smallest CTG known allele, in an American Samoan individual. (CTG) > or = 19 alleles are the most frequent in Europeans followed by the populations of Asian origin and are absent or rare in Africans. To understand the evolution of CTG repeats, we have used haplotype data from the CTG repeat and Alu(+/-) locus. Our results are consistent with previous studies, which show that among individuals of Caucasian and Japanese origin, the association of the Alu(+) allele with CTG repeats of 5 and > or = 19 is complete, whereas the Alu(-) allele is associated with (CTG)11-16 repeats. However, these associations are not exclusive in non-Caucasian populations. Most significantly, we have detected the (CTG)5 repeat allele on an Alu(-) background in several populations including Native Africans. As no (CTG)5 repeat allele on an Alu(-) background was observed thus far, it was proposed that the Alu(-) allele arose on a (CTG)11-13 background. Our data now suggest that the most parsimonious evolutionary model is (1) (CTG)5-Alu(+) is the ancestral haplotype; (2) (CTG)5-Alu(-) arose from a (CTG)5-Alu(+) chromosome later in evolution; and (3) expansion of CTG alleles occurred from (CTG)5 alleles on both Alu(+) and Alu(-) backgrounds.

Biological Evolution↗
PubMed1996

Microevolution and genetic affinities among six Amerindian tribes of lower Central America: comparative genetic study of serum proteins.

We evaluate the pattern of genetic variation among native Mesoamerican Amerindians by the construction of a gene frequency map that reflects the past action of evolutionary forces. The analysis is based on the theory that genes of modern human populations carry the encoded history even of humans' remote past and their early wanderings around the globe. We examined the serum proteins TF, PI, F13B and AHSG on 491 samples of 6 Mesoamerican Amerindian tribes (Guaymi, Bribri, Cabecar, Teribe, Guatuso, and Huetar) and 2 tribal mixed samples (Teribe x Guaymi and Bribri x Cabecar). We find a distinct genetic pattern in the examined tribes that clearly separates the Mesoamerican Amerindians from other living Amerindian groups. The proteins, TF, PI, and AHSG proved to be especially rich in special genetically fixed variants and polymorphisms, and F13B proved to be a powerful genetic marker to distinguish human groups. Using Nei's distance D and Mahalanobis's D2, we compared the polymorphisms and allele frequencies at the four serum protein loci to discern degrees of similarity between the samples. These data are presented in the dendrograms computed by average linkage cluster analyses and in two kinds of unrooted phylogenetic trees, neighbor-joining trees and split decompositions. Estimations are made on Hardy-Weinberg equilibrium and on genetic diversity and average heterozygosity index.

Blood Proteins↗
PubMed1995

Lack of a BglII site at the 5' region of the PGK 1 locus: a new variant discovered in two Chibchan Amerindian groups from Costa Rica.

A new 3.8-kb allele at the 5' region of the PGK 1 locus detected by the probe pSPT/PGK is reported. This variant was discovered in the Cabecar and Guaymi, two Chibchan Amerindian groups of Costa Rica. So far, a polymorphism that consists of an EcoRI/BglI (1.3-kb) variable site within an EcoRI/BglII (1.7-kb) fragment when DNA is simultaneously digested with EcoRI, BglI and BglII is known to occur in black and Caucasian populations. These two alleles were also found in the Amerindians tested. The newly described band is due to the lack of the BglII site situated 1.7 kb downstream from the EcoRI site and to the cleavage of another BglII site 2.1 kb downstream from the lacking one. This variant might be restricted to some Amerindian groups and perhaps also to Asiatic populations. Thus, it could be a useful marker in evolutive studies and for forensic applications. Moreover, the presence of a third allele in populations with Amerindian ancestry can increase the heterozygosity of the region disclosed by the pSPT/PGK probe, thus improving its application in issues dealing with X-chromosome activation ratios in females.

Costa Rica↗
PubMed1994

Mitochondrial DNA "clock" for the Amerinds and its implications for timing their entry into North America.

Students of the time of entry of the ancestors of the Amerinds into the New World are divided into two camps, one favoring an "early" entry [more than approximately 30,000 years before the present (YBP)], the other favoring a "late" entry (less than approximately 13,000 YBP). An "intermediate" date is unlikely for geological reasons. The correlation of the appropriate data on mtDNA variation in Amerinds with linguistic, archaeological, and genetic data offers the possibility of establishing a time frame for mtDNA evolution in Amerinds. In this paper, we estimate that the separation of the Chibcha-speaking tribes of Central America from other linguistic groups/nascent tribes began approximately 8000-10,000 YBP. Characterization of the mtDNA of 110 Chibcha speakers with 14 restriction enzymes leads on the basis of their time depth to an estimated mtDNA nucleotide substitution rate for Amerinds of 0.022-0.029% per 10,000 years. As a first application of this rate, we consider the mtDNA variation observed in 18 Amerind tribes widely dispersed throughout the Americas and studied by ourselves with the same techniques, and we estimate that if the Amerinds entered the New World as a single group, that entry occurred approximately 22,000-29,000 YBP. This estimate carries a large but indeterminate error. The mtDNA data are thus at present equivocal with respect to the most likely times of entry of the Amerind into the New World mentioned above but favor the "early" entry hypothesis.

Anthropology↗
PubMed1994

Direct screening of a mitochondrial DNA deletion valuable for Amerindian evolutionary research.

A rapid, simple restriction isotyping method is described for the direct screening of a previously characterized Amerindian mitochondrial DNA (mtDNA) marker consisting of a 6-bp "Huetar" deletion. In a sample of 31 maternally non-related Chibchan Amerindian Bribri from Costa Rica, this deletion was present in 74%, arguing for the usefulness of this private polymorphism for Amerindian taxonomic research.

Base Sequence↗
PubMed1994

Helicobacter pylori in a Costa Rican dyspeptic patient population.

Gastric biopsies from 65 Costa Rican dyspeptic patients were investigated for the presence of Helicobacter pylori DNA by polymerase chain reaction (PCR) amplification of 16S rRNA sequences. Both frozen and paraffin-embedded samples were used, and the results were compared with bacterial culture and histological examination. Helicobacter pylori DNA was detected by PCR in 60 (92%) of the patients, and Helicobacter pylori strains confirmed by PCR could be isolated from 37 of them. Altogether, 59 patients were shown to be infected using the combination of culture and histology as the reference method. The sensitivity of PCR analysis of frozen material was 98% (58/59). The PCR analysis of paraffin-embedded samples seemed less reliable than that of frozen biopsy material.

Adult↗
PubMed1994

mtDNA variation in the Chibcha Amerindian Huetar from Costa Rica.

The genetic variation in a Chibcha-speaking Amerindian tribe from lower Central America, the Huetar, was analyzed using nucleotide sequences of the hypervariable segments of the mitochondrial DNA (mtDNA) control region, the frequencies of 10 Amerindian-specific mtDNA haplotypes, and the regional distribution of private protein polymorphisms. The sequencing of 713 base pairs (bp) in the control regions of 27 individuals revealed 11 distinct lineages. These were defined by 24 variable sites and a 6-bp deletion between nucleotide pairs (np) 106 and 111. The 6-bp deletion is a new mtDNA marker that will be valuable for Amerindian taxonomic research. Control region sequences and mtDNA haplotype analyses reveal that Huetar mtDNAs are distributed in "Amerindian clusters" A, B, and D. A maximum-likelihood phylogenetic tree suggests a single origin for the 6-bp Huetar deletion in the sample. mtDNA haplotype analysis and the presence of previously characterized private protein variants (PEPA*F, TF*DCHI, and the absence of DI*A) show that the Huetar harbor polymorphisms of considerable antiquity, suggesting an early divergence from the regional founder gene pool for this population. The data also reflect a drastic constriction in population size, an evolutionary event with a proposed central effect on Huetar genetic structure.

Base Sequence↗
PubMed1993

[Genetic diversity and racial mixture in Amerindians from Costa Rica and Panama].

The genetic diversity of nine Amerindian tribes (Boruca, Bokota, Bribrí, Cabecar, Guatuso, Guaymí, Huetar, Kuna and Teribe) from Costa Rica and Panama were analyzed using 48 loci of enzymatic systems, blood groups and serum proteins. The average heterozygosity (H) and the frequency of polymorphisms (P) for this assemblage are relatively low (H = -0.055; P = 0.217). The genetic differentiation within tribes is also low with the exception of the Cabecar (Gst = 0.049). However it is high between tribes (Gst = 0.073). These populations have some racial admixture and negro and caucasian genes are present in different frequencies (1-30%) depending on their ecological and cultural background. Mating systems and random genetic drift should explain these results. In a broad sense the genetic diversity of these Chibchan tribes are similar to others from South America which use different languages.

Costa Rica↗
PubMed1992

["Cholos de Coclé": determination of their racial mixture and genetic origins].

We have found, in this first genetic study of a supposedly admixed Panamanian population, that the cultural group known as "cholos of Coclé" constitute a trihybrid mixture, whose genetic pool has the following composition: 44% Amerindian, 38% Caucasoid and 18% Negroid. Similarly, we have detected Amerindian genes, such as LDHB--Gua and TFchi, in proportions that relate this population with the extant Ngawbé (Guaymí). Nevertheless, the very high frequency of variant PEPA--KUN seems to indicate the genetic contribution of Amerindian populations from Eastern Panama, possibly from the extinct indigenous group cueva. This variant is frequently found among the present-day Kuna, but has not been detected among Nagawbé and Buglé.

Humans↗
PubMed1992

Microevolution of the Chibcha-speaking peoples of lower Central America: rare genes in an Amerindian complex.

Models are developed for the survival, history, and spread of variant alleles, in order to consider what can, and what cannot, be inferred from this type of data. The high variances of the processes involved, and questions of sampling, place severe limitations on inferences. Nonetheless, by combining information on a number of rare variants observed in a group of interrelated populations, reliable qualitative inferences are possible. These ideas and models are developed in the context of data on five rare variants and six private polymorphisms observed in eight Chibcha-speaking tribes of Costa Rica and Panama. The decline and fragmentation of the Amerindian populations of Central America over the last 300 years create considerable difficulties in attempting inference of past genetic events. However, these tribes have been well studied genetically, anthropologically, and linguistically and thus provide an excellent framework for the study of rare-variant spread.

Biological Evolution↗