Influence of the 48867A>C (Asp358Ala) IL6R polymorphism on response to a lifestyle modification intervention in individuals with metabolic syndrome.

We evaluated the response of individuals with metabolic syndrome to lifestyle modification intervention and examined the influence of the 48867A>C (Asp358Ala) IL6R (rs2228145) polymorphism on this response. Participants were randomly divided into two groups: NI, nutritional intervention; NIE, nutritional intervention and exercise practice. Intervention lasted three months and participants completed a comprehensive evaluation and had blood collected for biochemical measurements. Eighty-two sedentary individuals with at least three criteria for metabolic syndrome were included. Comparing metabolic syndrome parameters before and after intervention, a reduction of waist circumference was observed, although significant only for AA and AC genotypes. Also, a decrease in triglyceride levels was observed (significant for AA genotype individuals; for the AC genotype, only in the NIE group). Significant reduction of fasting glucose level was observed in all AA genotype individuals; for the AC genotype, only in the NI group. Systolic blood pressure showed significant reduction in AA and AC genotype individuals. After three months of lifestyle modification intervention, improvement in some of the metabolic syndrome parameters was observed, some associated with the IL6R genotype. At enrollment, participants with genotypes AA and AC showed more severe conditions regarding metabolic syndrome inclusion criteria, supporting previous reports that the A allele is a genetic risk factor. These individuals, however, had a better response to intervention compared to individuals with the CC genotype, suggesting that nutritional control and exercise practice could prevent risks associated with metabolic syndrome more efficiently in individuals bearing the A allele.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2011-31 July 2011.

This article documents the addition of 112 microsatellite marker loci and 24 pairs of single nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Agelaius phoeniceus, Austrolittorina cincta, Circus cyaneus, Circus macrourus, Circus pygargus, Cryptocoryne × purpurea Ridl. nothovar. purpurea, Mya arenaria, Patagioenas squamosa, Prochilodus mariae, Scylla serrata and Scytalopus speluncae. These loci were cross-tested on the following species: Cryptocoryne × purpurea nothovar. purpurea, Cryptocoryne affinis, Cryptocoryne ciliata, Cryptocoryne cordata var. cordata, Cryptocoryne elliptica, Cryptocoryne griffithii, Cryptocoryne minima, Cryptocoryne nurii and Cryptocoryne schulzei. This article also documents the addition of 24 sequencing primer pairs and 24 allele-specific primers or probes for Aphis glycines.

Mitochondrial control region haplotypes of the South American sea lion Otaria flavescens (Shaw, 1800).

The South American sea lion, Otaria flavescens, is widely distributed along the Pacific and Atlantic coasts of South America. However, along the Brazilian coast, there are only two nonbreeding sites for the species (Refúgio de Vida Silvestre da Ilha dos Lobos and Refúgio de Vida Silvestre do Molhe Leste da Barra do Rio Grande), both in Southern Brazil. In this region, the species is continuously under the effect of anthropic activities, mainly those related to environmental contamination with organic and inorganic chemicals and fishery interactions. This paper reports, for the first time, the genetic diversity of O. flavescens found along the Southern Brazilian coast. A 287-bp fragment of the mitochondrial DNA control region (D-loop) was analyzed. Seven novel haplotypes were found in 56 individuals (OFA1-OFA7), with OFA1 being the most frequent (47.54%). Nucleotide diversity was moderate (π = 0.62%) and haplotype diversity was relatively low (67%). Furthermore, the median joining network analysis indicated that Brazilian haplotypes formed a reciprocal monophyletic clade when compared to the haplotypes from the Peruvian population on the Pacific coast. These two populations do not share haplotypes and may have become isolated some time back. Further genetic studies covering the entire species distribution are necessary to better understand the biological implications of the results reported here for the management and conservation of South American sea lions.

Mitochondrial control region haplotypes of the South American sea lion Otaria flavescens (Shaw, 1800)

The South American sea lion, Otaria flavescens, is widely distributed along the Pacific and Atlantic coasts of South America. However, along the Brazilian coast, there are only two nonbreeding sites for the species (Refúgio de Vida Silvestre da Ilha dos Lobos and Refúgio de Vida Silvestre do Molhe Leste da Barra do Rio Grande), both in Southern Brazil. In this region, the species is continuously under the effect of anthropic activities, mainly those related to environmental contamination with organic and inorganic chemicals and fishery interactions. This paper reports, for the first time, the genetic diversity of O. flavescens found along the Southern Brazilian coast. A 287-bp fragment of the mitochondrial DNA control region (D-loop) was analyzed. Seven novel haplotypes were found in 56 individuals (OFA1-OFA7), with OFA1 being the most frequent (47.54 percent). Nucleotide diversity was moderate (π = 0.62 percent) and haplotype diversity was relatively low (67 percent). Furthermore, the median joining network analysis indicated that Brazilian haplotypes formed a reciprocal monophyletic clade when compared to the haplotypes from the Peruvian population on the Pacific coast. These two populations do not share haplotypes and may have become isolated some time back. Further genetic studies covering the entire species distribution are necessary to better understand the biological implications of the results reported here for the management and conservation of South American sea lions.

Inter-species hybridization among Neotropical cats of the genus Leopardus, and evidence for an introgressive hybrid zone between L. geoffroyi and L. tigrinus in southern Brazil.

Natural hybrid zones between distinct species have been reported for many taxa, but so far, few examples involve carnivores or Neotropical mammals in general. In this study, we employed mitochondrial DNA (mtDNA) sequences and nine microsatellite loci to identify and characterize a hybrid zone between two Neotropical felids, Leopardus geoffroyi and L. tigrinus, both of which are well-established species having diverged from each other c. 1 million years ago. These two felids are mostly allopatric throughout their ranges in South America, with a narrow contact zone that includes southern Brazil. We present strong evidence for the occurrence of hybridization between these species and identify at least 14 individuals (most of them originating from the geographical contact zone) exhibiting signs of interspecific genomic introgression. The genetic structure of Brazilian L. tigrinus populations seems to be affected by this introgression process, showing a gradient of differentiation from L. geoffroyi correlated with distance from the contact zone. We also corroborate and extend previous findings of hybridization between L. tigrinus and a third related felid, L. colocolo, leading to an unusual situation for a mammal, in which the former species contains introgressed mtDNA lineages from two distinct taxa in addition to its own.

DNA sequence analysis and the phylogeographical history of the rodent Deltamys kempi (Sigmodontinae, Cricetidae) on the Atlantic Coastal Plain of south of Brazil.

The rodent Deltamys kempiThomas, 1917 is found on the Coastal Plain - a recently formed geographic region located on Brazil's south-east coast. Considering that Deltamys is the only South American sigmodontine with a sex chromosome system of type X(1)X(1)X(2)X(2)/X(1)X(2)Y, this investigation was focused on the phylogeographic history of this taxon by using gene sequence analysis, trying to clarify when Deltamys differentiated, what was its centre of diversification, and what were the probable routes it used to reach its present distribution. We analysed sequences of the mitochondrial cytochrome b gene and nuclear recombination activating gene 2, performed cranial measurements and searched for centric fusions in individuals collected in distinct localities. The results, clearly demonstrate that D. kempi, on the Coastal Plain, divided into two groups, one occupying a small portion to the north of this region and the other spreading widely to the south. In this process, the phenomena of marine transgression and regressions which moulded its habitat, together with the occurrence of successive chromosomal rearrangements, were certainly the fundamental factors in shaping D. kempi diversification.

Uniparental (mtDNA, Y-chromosome) polymorphisms in French Guiana and two related populations--implications for the region's colonization.

Blood samples collected in four Amerindian French Guiana populations (Palikur, Emerillon, Wayampi and Kali'na) in the early 1980s were screened for selected mtDNA and Y-chromosome length polymorphisms, and sequenced for the mtDNA hypervariable segment I (HVS-I). In addition, two other Amerindian populations (Apalaí and Matsiguenga) were examined for the same markers to establish the genetic relationships in the area. Strong dissimilarities were observed in the distribution of the founding Amerindian haplogroups, and significant p-values were obtained from F(ST) genetic distances. Interpopulation similarities occurred mainly due to geography. The Palikur did not show obvious genetic similarity to the Matsiguenga, who speak the same language and live in a region from where they could have migrated to French Guiana. The African-origin admixture observed in the Kali'na probably derives from historical contacts they had with the Bushinengue (Noir Marron), a group of escaped slaves who now lead independent lives in a nearby region. This analysis has identified significant clues about the Amerindian peopling of the North-East Amazonian region.

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.

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

N-acetyltransferase 2 (NAT2), an important enzyme in clinical pharmacology, metabolizes antibiotics such as isoniazid and sulfamethoxazole, and catalyzes the transformation of aromatic and heterocyclic amines from the environment and diet into carcinogenic intermediates. Polymorphisms in NAT2 account for variability in the acetylator phenotype and the pharmacokinetics of metabolized drugs. Native Americans, settled in rural areas and large cities of Latin America, are under-represented in pharmacogenetics studies; therefore, we sequenced the coding region of NAT2 in 456 chromosomes from 13 populations from the Americas, and two from Siberia, detecting nine substitutions and 11 haplotypes. Variants *4 (37%), *5B (23%) and *7B (24%) showed high frequencies. Average frequencies of fast, intermediate and slow acetylators across Native Americans were 18, 56 and 25%, respectively. NAT2 intra-population genetic diversity for Native Americans is higher than East Asians and similar to the rest of the world, and NAT2 variants are homogeneously distributed across native populations of the continent.

Worldwide genetic variation at the 3'-UTR region of the LDLR gene: possible influence of natural selection.

The low density lipoprotein receptor gene (LDLR) contains many Alu insertions, and is especially Alu-rich at its 3'-untranslated region (3'-UTR). Previous studies suggested that the LDLR 3'-UTR could regulate gene expression by the stabilization of its mRNA. Given the faster Alu evolutionary rate, and wondering about its consequences in a possibly regulatory locus, we have studied approximately 800 bp of 222 chromosomes from individuals of African, Asian, Caucasian and Amerind ancestry, to better understand the evolution of the worldwide genetic diversity at this locus. Twenty-one polymorphic sites, distributed in 15 haplotypes, were found. High genetic diversity was observed, concentrated in one Alu insertion (Alu U), which also shows a fast evolutionary rate. Genetic diversity is similar in all populations except Amerinds, suggesting a bottleneck during the peopling of the American continent. Three haplotype clusters (A, B, C) are distinguished, cluster A being the most recently formed (approximately 500,000 years ago). No clear geographic structure emerges from the haplotype network, the global F(st) (0.079) being lower than the average for the human genome. When ancestral population growth is taken into account, neutrality statistics are higher than expected, possibly suggesting the action of balancing selection worldwide.

Phylogenetic information in polymorphic L1 and Alu insertions from East Asians and Native American populations.

This study attempts to ascertain genetic affinities between Native American and East Asian populations by analyzing four polymorphic Alu insertions (PAIs) and three L1 polymorphic loci. These two genetic systems demonstrated strong congruence when levels of diversity and genetic distances were considered. Overall, genetic relatedness within Native American groups does not correlate with geographical and linguistic structure, although strong grouping for Native Americans with East Asians was demonstrated, with clear discrimination from African and European groups. Most of the variation was assigned to differences occurring within groups, but the interpopulation variation found for South Amerindians was recognizably higher in comparison to the other sampled groups of populations. Our data suggest that bottleneck events followed by strong influence of genetic drift in the process of the peopling of the Americas may have been determinant factors in delineating the genetic background of present-day South Amerindians. Since no clear subgroups were detected within Native Americans and East Asians, there is no indication of multiple waves in the early colonization of the New World.

B-F DNA sequence variability in Brazilian (blue-egg Caipira) chickens.

A total of 100 chickens from the Brazilian (blue-egg Caipira) native breed were studied in relation to exon 2 of the B-F genes of the major histocompatibility complex (MHC) region. After a first screening on 100 birds, 22 animals were selected for amplification, cloning and sequencing experiments of exons 2-4 (a total of 1048 bp) of their DNA. Twenty-three sequences were obtained, of which at least 10 appear novel. Inferred protein sequences were compared with those previously described, totalling 41 different sequences with amino acid changes in 33 of the 88 sites in alpha1, and 34 of the 91 sites in alpha2 domains. Allele expression was investigated in these animals through cloning experiments. The blue-egg Caipira chickens may provide a source of novel B-F alleles for genetic improvement programmes.

Mitochondrial DNA and Alu insertions in a genetically peculiar population: the Ayoreo Indians of Bolivia and Paraguay.

A total of 91 Ayoreo individuals previously studied for blood groups and protein markers, living in two Bolivian and one Paraguayan communities, were extensively investigated in relation to the hypervariable 1 segment of the control and eight coding regions of their mitochondrial DNA (mtDNA). They show an extremely reduced mtDNA variability, the observed haplotypes being classifiable in just two haplogroups (C and D). They were also variously studied in relation to six Alu insertions; in this case, however, the prevalences found did not depart markedly from those obtained in other populations of this ethnic group. To assess the Ayoreo position in relation to these populations, 11 other groups that had also been studied for these systems and for blood groups and proteins were selected. The dendrograms obtained with two of the three sets of markers showed distinct patterns, but the Ayoreo were placed in a central position in both the blood group + proteins and Alu insertions trees. Therefore, they are clearly distinct in relation to their mtDNA only, suggesting a strong founder effect and/or random loss of variability in this system.

Extremely limited mitochondrial DNA variability among the Aché Natives of Paraguay.

BACKGROUND: The Aché Natives are an especially interesting group of people, due to their distinctive morphological aspect and the fact that only in the last three decades have they established more permanent contact with outside populations. The objectives of the present study were: (a) to verify their distinctiveness in relation to mitochondrial DNA (mtDNA) variability; (b) to ascertain whether the pattern observed was congruent with other genetic studies performed among them; and (c) to establish historical inferences that would explain the eventual similarities or differences. SUBJECTS AND METHODS: Sample collection was made at two localities in eastern Paraguay. DNA from 64 maternally unrelated subjects were tested in relation to the mtDNA hypervariable segment 1 (HVS-1) by automatic sequencing. RESULTS: Fifty-six individuals presented exactly the same haplogroup B founder haplotype; another differed from it by a single transition polymorphism at site 16362, while six other subjects showed an identical haplogroup A founding haplotype. An A/G heteroplasmy at the 16269 site was seen in one haplogroup B individual, probably due to a somatic mutation. CONCLUSIONS: The Aché present distinctive differences and reduced mtDNA HVS-1 variability compared to other South American Natives. Similar differences were observed for other genetic systems. At present it is not clear whether their peculiarities already existed in their founding populations or whether they were secondarily acquired due to a long period of isolation in the humid, subtropical forest.

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.

Evolutionary implications of infra- and interspecific molecular variability of pathogenesis-related proteins

We have examined phylogenetic relationships in seven pathogenesis-related (PR) protein families. Within-family comparisons involved 79 species, 166 amino acid sequences, and 1,791 sites. For 37 species, 124 different PR isoforms were identified (an average of 3.3 per species). Thirty-one of the 37 species investigated tended to cluster together (84 percent). Of the 17 clusters distinguished in the seven phylogenetic trees, 10 (59 percent) were in agreement with their taxonomic status, ascertained at the family level. The strong similarities among the intraspecific forms, as compared to interspecific differences, argue for some kind of gene conversion, but the rare occurrence of widely different isoforms also suggests diversifying selection. PRs 1, 6, and 4 seem to be less differentiated than PRs 3, 2, 10, and 5.

Evolutionary implications of intra- and interspecific molecular variability of pathogenesis-related proteins.

We have examined phylogenetic relationships in seven pathogenesis-related (PR) protein families. Within-family comparisons involved 79 species, 166 amino acid sequences, and 1,791 sites. For 37 species, 124 different PR isoforms were identified (an average of 3.3 per species). Thirty-one of the 37 species investigated tended to cluster together (84%). Of the 17 clusters distinguished in the seven phylogenetic trees, 10 (59%) were in agreement with their taxonomic status, ascertained at the family level. The strong similarities among the intraspecific forms, as compared to interspecific differences, argue for some kind of gene conversion, but the rare occurrence of widely different isoforms also suggests diversifying selection. PRs 1, 6, and 4 seem to be less differentiated than PRs 3, 2, 10, and 5.

Alu insertions versus blood group plus protein genetic variability in four Amerindian populations.

BACKGROUND: Do the population relationships obtained using DNA or blood group plus protein markers remain the same or do they reveal different patterns, indicating that the factors which influence genetic variation at these two levels of analysis are diverse? Can these markers shed light on the biological classification of the Aché, a Paraguayan tribe which only recently established more permanent contacts with non-Indians? SUBJECTS AND METHODS: To consider these questions we typed 193 individuals from four Amerindian tribes in relation to 12 Alu polymorphisms (five of them never studied in these populations), while 22 blood group plus protein systems were studied among the Aché. These data were then integrated with those previously available (blood groups plus proteins) for the three other populations. DNA extraction and amplification, as well as the other laboratory procedures, were performed using standard methods currently in use in our laboratory. The genetic relationships were obtained using the D(A) distance, and the trees were constructed by the neighbour-joining method, both developed by M. Nei and collaborators. Reliability of the trees was tested by bootstrap replications. Other population variability values were also determined using Nei's methods. RESULTS: Alu polymorphism was observed in all populations and for most of the loci; in the seven systems from which we could compare our results with those of other Amerindian groups agreement was satisfactory. Unusual findings on the blood group plus protein systems of the Aché were a very low (5%) HP*1 frequency and the presence of the C(W) phenotype in the Rh blood group. The intertribal patterns of relationship and other aspects of their variation were remarkably congruent in the two sets (Alu; blood group plus protein) of systems. CONCLUSIONS: The answer to the first question posed above is affirmative. However, the problem of whether the Aché derived from a Gê group that preceded the Guarani colonization of Paraguay, or are just a differentiated Guarani group, could not be answered with the genetic information available; the second hypothesis seems more likely at present, but the point to be emphasized is the striking genetic distinctiveness of the Aché as compared to other Amerindians.

Genetic, geographic, and linguistic variation among South American Indians: possible sex influence.

To better understand the relationship between genetic variability, geographical distance, and linguistic affiliation in South Amerinds, and to elucidate whether the migration rate is the same for both sexes, spatial autocorrelation, Mantel's test, and F(ST) analyses were performed in four sets of populations and alleles (group 1: 48 populations, 12 alleles; group 2: 16 (all belonging to the Tupi linguistic group) and 12; group 3: 21 and 17; and group 4: 28 and 4 haplotypes). Groups 1-3 included blood group and protein (i.e., serum protein, red cell enzymes, and immunoglobulin systems), while group 4 was concerned with mitochondrial DNA (mtDNA) only. The latter set was also subjected to a molecular analysis of variance (AMOVA) evaluation. The frequencies of statistically significant correlograms were lower than those obtained in other populations when the blood groups and protein systems were considered, but 3 of the 4 mtDNA haplogroups gave suggestions of population structure. The variability in this organelle is also significantly correlated with language when geography is held constant. Migration per generation is generally low, but higher estimates were obtained for females. The AMOVA results suggest that populations whose members speak the same language are genetically homogeneous and may be viewed as the ultimate evolutionary unit at this level of analysis.

Phylogeographic patterns and evolution of the mitochondrial DNA control region in two neotropical cats (Mammalia, felidae).

The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation of the Panamanian land bridge 3-5 million years ago. Patterns of population genetic divergence of each species were studied by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed, identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography, population genetic structure, and demographic history were used to formulate conservation recommendations for these species. In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region in closely related felids.