Genetic structure and gene flow in Gran Chaco populations of Argentina: evidence from Y-chromosome markers

The Gran Chaco region of central South America has been settled by humans for only the last 4,000-5,000 years. To investigate population structure and variation in this region's indigenous population, we scored males from tribes of the Argentinean part of the Gran Chaco (Pilagá, Wichí, and Toba, representing two major language groups, the Mataco and Guaycurú) for a number of Y-chromosome polymorphisms. The markers included eight microsatellites (DYS19, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, and DYS439) and the unique native American single nucleotide polymorphism, DYS199. Sixty males (77%) from the total sample carried the DYS199T chromosome, and these were the focus of the present analysis. Unlike most other native Americans, Gran Chaco males show a moderate level of diversity at the DYS19 locus but still less than that seen in non-native Americans. The FST value for Y-chromosome markers in Gran Chaco was 0.107, a value that is more than double that found for mtDNA haplogroups in the same tribes but is not particularly high compared with other Y-chromosome studies. Phylogenetic trees based on all eight microsatellites showed relatively poor correlation of the tribes with either geography or language, and this is possibly explained by their ecology. They are seasonal hunters living in small bands, and under such circumstances drift will be a powerful evolutionary force. An UPGMA tree based on five microsatellites (DYS19, DYS390, DYS391, DYS392, and DYS393), however, showed a more positive relationship, suggesting that DYS437, DYS438, and DYS439 may behave differently from the other microsatellites. No association was found between maternal and paternal lineage distributions. The time to the most recent common ancestor of the DYS199T chromosome is calculated to lie between 13,000 and 26,000 years. This range is consistent with estimates from other Y-chromosome studies as well as with estimates from mtDNA and the archeology of the colonization of South America. We conclude that the male lineages present in the contemporary Gran Chaco population reflect the level of diversity found in South America and that the region's male founders did not carry a restricted gene pool.     

Is the genetic structure of Gran Chaco populations unique? Interregional perspectives on native South American mitochondrial DNA variation

This study reevaluates the hypothesis in Demarchi et al. (2001 Am. J. Phys. Anthropol. 115:199-203) that Gran Chaco peoples demonstrate a unique pattern of genetic diversity due to a distinct regional population history. Specifically, they found populations in the central part of the Gran Chaco, or Central Chaco, to have higher within- and lower between-population mitochondrial DNA (mtDNA) haplogroup frequency variation compared to populations in other South American regions. To test this hypothesis of regional uniqueness, we applied analytical and simulation methods to mtDNA first hypervariable (HVI) region sequence data from a broad set of comparative South and Central American population samples. Contrary to the results of Demarchi et al. (2001 Am. J. Phys. Anthropol. 115:199-203), we found that the Gran Chaco's regional within-population diversity is about average among regions, and populations are highly differentiated from each other. When we limited the scale of analysis to the Central Chaco, a more localized subregion of the Gran Chaco, our results fell more in line with the original findings of Demarchi et al. (2001 Am. J. Phys. Anthropol. 115:199-203). Still, we conclude that neither the Gran Chaco regional pattern, nor the Central Chaco subregional pattern, is unique within South America. Nonetheless, the Central Chaco pattern accords well with the area's history, including pre-European contact lifeways and the documented historical use of the area as an interregional crossroads. However, we cannot exclude post-European contact disruption of traditional mating networks as an equally plausible explanation for the observed diversity pattern. Finally, these results additionally inform broader models of South American genetic diversity. While other researchers proposed an east-west continental division in patterns of genetic variation (e.g., Fuselli et al. 2003 Mol. Biol. Evol. 20:1682-1691), we found that in the geographically intermediate Central Chaco, a strict east-west divide in genetic variation breaks down. We suggest that future genetic characterizations of the continent, and subsequent interpretations of evolutionary history, involve a broad regional sampling of South American populations.     

Mitochondrial DNA haplogroups in Amerindian populations from the Gran Chaco.

Mitochondrial DNA from 141 individuals was typed for diagnostic restriction sites and the 9-bp region V deletion to examine the distribution of the founding mtDNA lineage haplotypes in three Amerindian populations (Mataco, Toba, and Pilagá) who currently inhabit the Argentinian part of the Gran Chaco. All four lineages were identified in the three tribes and four population samples studied. Disregarding ethnic or geographic origin, haplogroups B and D exhibit high incidence among the Gran Chaco inhabitants, whereas haplogroups A and C are present in a lower frequency. Three individuals possess none of the characteristic markers and, therefore, could not be assigned to one of those lineages. A neighbor-joining representation of F(ST) distances reflects the current geographic location of the populations, and this also corresponds to their historic distribution. After separating South America into four major regions (Tropical Forest, Andes, Gran Chaco, and Patagonia-Tierra del Fuego), the Gran Chaco populations present the highest average intragroup variability (Hs = 0.64) as well as the lowest intergroup diversity (G(')(ST) = 0.06). These findings suggest high levels of gene flow among the Chaco tribes, as well as with neighbor populations from outside the region.     

Autosome STRs in native South America-Testing models of association with geography and language

Information on one Ecuadorian and three Peruvian Amerindian populations for 11 autosomal short tandem repeat (STR) loci is presented and incorporated in analyses that includes 26 other Native groups spread all over South America. Although in comparison with other studies we used a reduced number of markers, the number of populations included in our analyses is currently unmatched by any genome-wide dataset. The genetic polymorphisms indicate a clear division of the populations into three broad geographical areas: Andes, Amazonia, and the Southeast, which includes the Chaco and southern Brazil. The data also show good agreement with proposed hypotheses of splitting and dispersion of major language groups over the last 3,000 years. Therefore, relevant aspects of Native American history can be traced using as few as 11 STR autosomal markers coupled with a broad geographic distribution of sampled populations.     

Deforestation and cattle ranching drive rapid range expansion of capybara in the Gran Chaco ecosystem

Anthropogenic habitat alteration has the capacity to alter the distribution of species. Capybara (Hydrochoerus hydrochaeris) are a widely distributed rodent throughout most of South America, but are restricted to areas of standing water. As the Gran Chaco ecosystem of Paraguay is converted from dry tropical forest to pastureland, we hypothesize that this alteration creates potential for invasion by capybara into newly fragmented areas. We surveyed throughout the Chaco to estimate the distribution of capybara, and we collected noninvasive genetic samples. We used ecological niche modeling based on six environmental or climatic variables, and we modeled both the current distribution of capybara and the distribution of capybara 80 years ago. We then verified the hypothesized demographic signal generated with our model using phylogeographic analyses of 386 bp of the mtDNA control region. Comparison of present and past models suggested that populations expanded into the Gran Chaco after forest was converted to pastureland. Analyses of the mitochondrial D‐loop supported the rapid range expansion scenario. We also found evidence of secondary contact of two distinct phylogroups which had previously been disjunct. Anthropogenic land transformation appeared to be a major factor influencing the distribution, as predicted by the niche model and confirmed by genetic data. Habitat modification altered connectivity of populations across the landscape. In addition, long separated clades of capybara are now admixed throughout the Paraguayan Chaco. The invasion of a large bodied herbivore into the High Chaco region may exacerbate the degradation of forest and prevent forest regeneration. As the reservoir host of several zoonotic diseases, the expansion and contact of two previously disjunct capybara populations has implications for disease emergence.     

The consumption ofTypha domingensis pers. (Typhaceae) Pollen among the ethnic groups of the Gran Chaco, South America

The gathering of Typha domingensis pollen and the modes of preparation and consumption edible products with it by seven ethnic groups of the Gran Chaco (Chulupí, Lengua, Maká, Mataco, Pilagá, Toba and Toba-Pilagá) in Argentina and Paraguay are described in this paper, together with those product’s local names and chemical compositions. Pollen provides an excellent food for those groups, because of both its nutritional value and its availability in periods when there is a scarcity of fruits and vegetables. The ethnic groups of the Gran Chaco do not eat any kind of pollen other than that ofT. domingensis.     

Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

Loss of mammalian species from the South American Gran Chaco: empty savanna syndrome?

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Species identification and genetic structure of threatened seahorses in Gran Canaria Island (Spain) using mitochondrial and microsatellite markers

A non-invasive DNA analysis of seahorse populations was carried out after extensive underwater surveys in Gran Canaria Island (Spain). In this geographical area, the presence of two species, Hippocampus hippocampus and H. guttulatus, has been previously reported. Sequencing of 16S ribosomal DNA (16S rDNA) was used for specific identification of live seahorses sampled in situ, as a previous step to evaluate genetic structure based on ten microsatellite markers. Phylogenetic analyses revealed the presence of a single species, H. hippocampus, in the seahorse communities found at Gran Canaria. No evidences of H. guttulatus or interspecific hybrids were found based on 16S rDNA and microsatellite data. The nuclear markers revealed low genetic diversity and lack of population structure across populations of Gran Canaria Island, with evidence of small population sizes. This study provides critical information to support conservation strategies of Gran Canaria seahorses.     

Infestation of rural houses by Triatoma infestans in the region of Los Llanos (La Rioja, Argentina)

Vectorial transmission of Chagas disease has been strongly reduced in most parts of the Southern Cone countries of South America, except in the Gran Chaco region of Argentina, Bolivia, and Paraguay. Given periodical interruptions of the vector control programmes in the endemic region of the Gran Chaco of Argentina, the vectorial transmission of the disease has been increasing during the last years. From the beginning of 2004, the provincial Ministry of Health of La Rioja, Argentina, started a vector control programme to cover the rural houses of the Los Llanos area in the southwestern area of the Gran Chaco region. This article reports the result of a standardized entomological survey and insecticide application against Chagas disease vectors in the intra and peridomestic structures of the rural houses of Los Llanos. A total of 4062 houses were inspected, of which 46.8% were found to be infested by Triatoma infestans. Infestation by vector species other than T. infestans was less than 0.5%(T. eratyrusiformis and T. platensis). Intradomestic infestation was found in 27.2%, whereas peridomestic infestation was found in 39.3% of the houses. The lowest figure of intradomestic infestation was 6.6% (Department F Varela), and the highest value of intradomestic infestation was 45.1% (Department Independencia). In spite of the demonstrated success of vector control elsewhere, this study shows that the vector populations are susceptible to pyrethroid insecticides in the southern area of the Gran Chaco of Argentina, that there still are regions where rural houses show heavy infestation by T. infestans associated with big peridomestic structures and that the vectorial transmission of the Chagas disease will continue, unless a sustained and well organized vector control effort is installed in the region.     

Molecular Population Genetics and Evolution of the Chagas’ Disease Vector Triatoma infestans (Hemiptera: Reduviidae)

Triatoma infestans (Klug) is the main vector of Chagas’ disease in the Southern Cone of Latin America between the latitudes 10° S and 46° S. The long-term effectiveness of the control campaigns is greatly dependent upon the vector population structure. Mitochondrial DNA (mtDNA) genes have been used in a number of T. infestans population genetic analyses. However, the maternally inherited markers as well as nuclear ribosomal DNA analyzed until the present exhibited low or limited levels of variation. Analyses based on microsatellite markers strongly supported the existence of some type of stratification in T. infestans populations and supported the hypothesis of vector population recovery from survivors of the insecticide-treated areas, highlighting the value of population genetic analyses in assessing the effectiveness of Chagas’ disease vector control programmes. Although phylogeographic studies have generally suggested a Bolivian Andean origin of T. infestans, they recovered two reciprocal monophyletic groups of T. infestans and Bolivian populations who were not basal as expected for an ancestral group. In addition, a non-Andean origin could not be excluded by mtDNA genealogies that included sylvatic bugs from Gran Chaco. On the other side, mitochondrial and microsatellite markers supported the hypothesis of two independent migration events of colonization and secondary contacts in southern South America. Since the phylogenetic analyses remain inconclusive, more sequences, not only from mitochondrial genes but also from nuclear genes, need to be examined.     

Genetic relationships of Plagioscion squamosissimus (Perciformes,Sciaenidae) from five Neotropical river basins evaluated using mitochondrial atpase6/8 gene sequences

The genetic relationships of native or introduced Plagioscion squamosissimus in five Brazilian Neotropical basins were evaluated using the mitochondrial atpase6/8 genes. Results revealed that the population of the Tocantins River basin is more basal than the native populations of the Amazon and Parnaíba River basins. Moreover, the populations of P. squamosissimus that were introduced in the São Francisco and upper Paraná River basins originated from the population of the Parnaíba River.     

Analysis of genetic diversity of Russian regional populations based on STR markers used in DNA identification

We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of DNA markers commonly used in Human DNA identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included markers officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allele frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and analyzed the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern Russian gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers in urban Russian populations. Therefore, the database of allele frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to southern and central Russian populations, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.     

Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations.

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.     

Genetic Diversity in Five Iranian Native Chicken Populations Estimated by Microsatellite Markers

Iranian chicken genetic resources are characterized by a long history and a vast diversity. This study represents the first results from the selection and evaluation of five polymorphic microsatellite markers for the genetic assessment of five native chicken populations located in the northwestern (West Azerbaijan), northern (Mazandaran), central (Isfahan, Yazd), and southern (Fars) provinces of Iran. The number of alleles ranged from three to six per microsatellite locus. All populations were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the Isfahan population (62%) and the greatest in the populations from West Azerbaijan and Mazandaran (79%). The largest Nei’s unbiased genetic distance was found between the Isfahan and Fars populations (0.696) and the smallest between the Mazandaran and Yazd populations (0.097). The Isfahan population was found to be the most genetically distant among all populations studied. These results serve as an initial step in the plan for genetic characterization and conservation of Iranian native chickens.     

Autosomal STR variation in five Austronesian populations

Human population characteristics at the genetic level are integral to both forensic biology and population genetics. This study evaluates biparental microsatellite markers in five Austronesian-speaking groups to characterize their intra- and interpopulation differences. Genetic diversity was analyzed using 15 short tandem repeat (STR) loci from 338 unrelated individuals from 5 Pacific islands populations, including the aboriginal Ami and Atayal groups from Taiwan, Bali and Java in Indonesia, and the Polynesian islands of Samoa. Allele frequencies from the STR profiles were determined and compared to other geographically targeted worldwide populations procured from recent literature. Hierarchical AMOVA analysis revealed a large number of loci that exhibit significant correspondence to linguistic partitioning among groups of populations. A pronounced divide exists between Samoa and the East (Formosa) and Southeast Asian (Bali and Java) islands. This is clearly illustrated in the topology of the neighbor-joining tree. Phylogenetic analyses also indicate clear distinctions between the Ami and Atayal and between Java and Bali, which belie the respective geographic proximities of the populations in each set. This differentiation is supported by the higher interpopulation variance components of the Austronesian populations compared to other Asian non-Austronesian groups. Our phylogenetic data indicate that, despite their linguistic commonalities, these five groups are genetically distinct. This degree of genetic differentiation justifies the creation of population-specific databases for human identification.     

中国汉族群体5个STR分子遗传标记

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Autosomal, mtDNA, and Y-chromosome diversity in Amerinds: pre- and post-Columbian patterns of gene flow in South America

To evaluate sex-specific differences in gene flow between Native American populations from South America and between those populations and recent immigrants to the New World, we examined the genetic diversity at uni- and biparental genetic markers of five Native American populations from Colombia and in published surveys from native South Americans. The Colombian populations were typed for five polymorphisms in mtDNA, five restriction sites in the beta-globin gene cluster, the DQA1 gene, and nine autosomal microsatellites. Elsewhere, we published results for seven Y-chromosome microsatellites in the same populations. Autosomal polymorphisms showed a mean G(ST) of 6.8%, in agreement with extensive classical marker studies of South American populations. MtDNA and Y-chromosome markers resulted in G(ST) values of 0.18 and 0.165, respectively. When only Y chromosomes of confirmed Amerind origin were used in the calculations (as defined by the presence of allele T at locus DYS199), G(ST) increased to 0.22. G(ST) values calculated from published data for other South American natives were 0.3 and 0.29 for mtDNA and Amerind Y chromosomes, respectively. The concordance of these estimates does not support an important difference in migration rates between the sexes throughout the history of South Amerinds. Admixture analysis of the Colombian populations suggests an asymmetric pattern of mating involving mostly immigrant men and native women.