How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data

Abstract In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.

Remembering the past - studies on evolution done by the genetics group at Universidade Federal do Rio Grande do Sul (UFRGS)

Abstract After a brief introduction about the factors that are involved in science development, and world and Brazilian evolutionary genetics, the studies developed in Porto Alegre in this area were reviewed. Four periods in the development of this group were distinguished: (a) Origins and first expansion (1949-1961); (b) Second expansion (1962-1988); (c) Third expansion (1989-2001); and (d) The last 15 years (2002-present). The international Porto Alegre Biological Evolution Workshops (PABEWs), with five biannual events from 2007 o 2015, were also mentioned. The final message stressed the importance of the maintenance of this and other Brazilian groups of research through adequate finance and recognition.

Molecular evolution and functional divergence of alcohol dehydrogenases in animals, fungi and plants

Abstract Alcohol dehydrogenases belong to the large superfamily of medium-chain dehydrogenases/reductases, which occur throughout the biological world and are involved with many important metabolic routes. We considered the phylogeny of 190 ADH sequences of animals, fungi, and plants. Non-class III Caenorhabditis elegans ADHs were seen closely related to tetrameric fungal ADHs. ADH3 forms a sister group to amphibian, reptilian, avian and mammalian non-class III ADHs. In fishes, two main forms are identified: ADH1 and ADH3, whereas in amphibians there is a new ADH form (ADH8). ADH2 is found in Mammalia and Aves, and they formed a monophyletic group. Additionally, mammalian ADH4 seems to result from an ADH1 duplication, while in Fungi, ADH formed clusters based on types and genera. The plant ADH isoforms constitute a basal clade in relation to ADHs from animals. We identified amino acid residues responsible for functional divergence between ADH types in fungi, mammals, and fishes. In mammals, these differences occur mainly between ADH1/ADH4 and ADH3/ADH5, whereas functional divergence occurred in fungi between ADH1/ADH5, ADH5/ADH4, and ADH5/ADH3. In fishes, the forms also seem to be functionally divergent. The ADH family expansion exemplifies a neofunctionalization process where reiterative duplication events are related to new activities.

The use and limits of ITS data in the analysis of intraspecific variation in Passiflora L. (Passifloraceae)

The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC.) Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora.

Genetic signatures of parental contribution in black and white populations in Brazil

Two hundred and three individuals classified as white were tested for 11 single nucleotide polymorphisms plus two insertion/deletions in their Y-chromosomes. A subset of these individuals (n = 172) was also screened for sequences in the first hypervariable segment of their mitochondrial DNA (mtDNA). In addition, complementary studies were done for 11 of the 13 markers indicated above in 54 of 107 black subjects previously investigated in this southern Brazilian population. The prevalence of Y-chromosome haplogroups among whites was similar to that found in the Azores (Portugal) or Spain, but not to that of other European countries. About half of the European or African mtDNA haplogroups of these individuals were related to their places of origin, but not their Amerindian counterparts. Persons classified in these two categories of skin color and related morphological traits showed distinct genomic ancestries through the country. These findings emphasize the need to consider in Brazil, despite some general trends, a notable heterogeneity in the pattern of admixture dynamics within and between populations/groups.

Patterns of molecular evolution in pathogenesis-related proteins

The genes encoding 13 classes of pathogenesis-related (PR) proteins were examined for positive selection using maximum-likelihood (ML) models of codon substitution. The study involved 194 sequences from 54 species belonging to 37 genera. Although the sizes of the sequences examined varied from 237 bp for PR12 to 1,110 bp for PR7, most classes (9 out of 13) contained sequences made up of more than 400 nucleotides. Signs of positive selection were obtained for sites in PR proteins 4, 6, 8, 9 and 15 using an ML-based Bayesian method and likelihood ratio tests. These results confirm the importance of positive selection in proteins related to defense mechanisms already observed in a wide array of organisms

Evolutionary change - patterns and processes

A presente revisão considerou: (a) os fatores que condicionaram a transição inicial entre não-vida e vida; (b) a estrutura e complexidade genômica em procariotos, eucariotos e organelas; (c) a genômica comparada dos cromossomos humanos; (d) a contribuição brasileira a alguns desses estudos. A compreensão do conflito dialético entre liberdade e organização é fundamental para dar significado aos padrões e processos da evolução orgânica.

Human T - cell lymphotropic virus type II in Guaraní Indians, Southern Brazil

O vírus linfotrópico de células T-humanas do tipo II (HTLV-II) é identificado em muitos grupos de ameríndios. No Brasil, tem sido encontrado em indivíduos da população urbana, bem como em índios oriundos da região Amazônica. Os Índios Guaraní, do Sul do país, foram investigados para infecção por HTLV-I/II. Três indivíduos, oriundos de uma amostra de 52 índios, demonstraram sororeatividade para HTLV-II (ensaio imunoenzimático e Western blot). Este estudo preliminar foi o primeiro a identificar a presença de infecção por HTLV-II em ameríndios do Sul do Brasil.

Interethnic variability and admixture in Latin America-social implications: [review]

Past and present attempts to classify and characterize the human biological variability are examined, considering the race concept, ethnic identification problems, assortative mating based on ethnicity, and historical genetics. In relation to the latter, a review is made of the methods presently available for admixture quantification and of previous studies aimed at the characterization of the parental continental contributions to Latin American populations, with emphasis in global evaluations of the Costa Rican and Brazilian gene pools. Finally, the question of racism and discrimination is considered, including the relation between human rights and affirmative actions. The right to equal opportunity should be strictly respected. Biological inequality has nothing to do with the ethical principle that someone's position in a given society should be an accurate reflection of her/his individual ability.

Ribeiro's typology, genomes, and Spanish colonialism, as viewed from Gran Canaria and Colombia

Four biallelic and six multiallelic Y-chromosome polymorphisms were investigated in 59 Gran Canarian, 60 North African Berber and 46 Spanish subjects. These new data were merged with equivalent literature information to obtain the parental Y-chrosomomal contribution in Gran Canarians, Colombians, and Venezuelans. The results were then compared, for Gran Canarians and Colombians, to those derived from autosomal and mtDNA. In both groups, the Spanish Y-chromosome contribution was much more marked than that estimated using mtDNA. This analysis showed a usual trend in the Spanish Colonial history, characterized by a demographic collapse of the aboriginal population, but with considerable introgression of genes through native women. In accordance to D. Ribeiro's typology for peoples subjected to Colonialism, the Y-chromosomes of these admixed populations are classified as transplanted, their mtDNA as witness, and their autosome sets as new.

Molecular variability in Amerindians: widespread but uneven information

A review was made in relation to the molecular variability present in North, Central, and South American Indian populations. It involved results from ancient DNA, mitochondrial DNA in extant populations, HLA and other autosomal markers, X and Y chromosome variation, as well as data from parasitic viruses which could show coevolutionary changes. The questions considered were their origin, ways in which the early colonization of the continent took place, types and levels of the variability which developed, peculiarities of the Amerindian evolutionary processes, and eventual genetic heterogeneity which evolved in different geographical areas. Although much information is already available, it is highly heterogeneous in relation to populations and types of genetic systems investigated. Unfortunately, the present trend of favoring essentially applied research suggest that the situation will not basically improve in the future

Perfil ético dos pesquisadores em genética / Ethical profile of genetics researchers

Säo apresentados dados relativos a uma enquete, realizada com 74 pesquisadores brasileiros em genética médica, sobre um conjunto padronizado de 52 questöes relacionadas a problemas éticos. A investigaçäo foi efetivada em 36 outros países e faz parte de um programa de avaliaçäo do tipo cultural-cruzado, que busca determinar, em nível mundial, diferenças e similaridades de opiniäo sobres estas especialistas da área. as comparaçöes internacionais ainda näo foram finalizadas mas os resultados obtidos säo cotejados com dados preliminares alcançados em outras naçöes e com um outro estudo do mesmo tipo, realizado no Brasil na década de 80. Entre esses especialistas há grande diversidade de opiniöes quanto aos temas abordados. Há consenso, no entanto, de que a quantidade de serviços genéticos oferecidos à populaçäo deve aumentar e que as leis que regem o aborto devem ser modificadas. Os depoimentos däo ênfase ao princípio da autonomia, desfavorecendo a obrigatoriedade de determinados procedimentos. Há apoio, porém, ao uso do DNA para a identificaçäo de criminosos

Demography, genetic diversity, and population relationships among Argentinean Mapuche Indians

Dados relativos a fertilidade, mortalidade e migraçäo de quatro comunidades de índios Mapuche localizadas em uma área linear na direçäo nordeste-sudoeste com 215 km de extensäo na Província de Rio Negro, Argentina, foram associados com a informaçäo genética fornecida por nove sistemas de grupos sangüíneos e os haplogrupos do DNA mitocondrial. Ambos os tipos de informaçäo apontam claramente para uma dicotomia, as quatro populaçöes sendo divididas em grupos de duas. O principal fator responsável por esta separaçäo é provavelmente graus diferentes de mistura com näo-índios. A variabilidade genética total foi muito similar em todos os grupos, aquela entre populações sendo de apenas 10 por cento deste valor. Foi confirmada a baixa prevalência do antígeno Diego(a) entre os Mapuche. O fato de que heterogeneidade genética significativa e conjuntos populacionais diversos foram observados em uma regiäo territorial täo pequena demonstra a sensibilidade dos enfoques demográfico e genético no esclarecimento da história humana.

James V. Neel and Latin America - or how scientific collaboration should be conducted

Apresentaçäo dos principais eventos relacionados com a vida de James V. Neel, um dos mais importantes geneticistas das últimas décadas, especialmente com referência à influência que ele exerceu na América Latina. É fornecida documentaçäo sobre o trabalho de campo que ele realizou no Brasil, e sobre os resultados do programa comum Ann Arbor-Porto Alegre de pesquisa.

Brazilian indian/non indian interactions and their effects

A short review was made of the history of the Brazilian population, starting with the Asians who colonized the region 30,000-40,000 years ago, and continuing with evaluations of the European, African, and neo-Asiatic immigration. Social aspects of the contact situation between Brazilian Indians and the surrounding society were briefly considered, as well as quantitative estimates of the amount of Amerindian genes present in neo-Brazilians. Special emphasis, however, was placed in the inverse gene flow (neo-Brazilian genes into Amerindians). In this case, two methods which quantify the degree of such admixture were employed, and the one considered to give better estimates was chosen. Although the correlation obtained between these admixture values and the number of years of more permanent contact with non-Indians yielded a low number (perhaps due to deficiencies in obtaining precise figures concerning years of contact), a clear correlation was found between the admixture estimates obtained in 39 Brazilian Indian tribes or populations and their location in degrees of longitude west. This is probably a reflection of the general neo-Brazilian east-west colonization movement. At present it is difficult to ascertain the degree of biological and cultural homogeneity that will be reached by Brazilian populations in the future. It is hoped, however, that a certain amount of diversity will be maintained, in a climate of mutual respect.

Beta s haplotype diversity in Afro-Americans, Africans, and Euro-Asiatics: an attempt at a synthesis

A review was made of the distribution of the five common betas haplotypes in eight Euro-Asian, 16 African and 12 American population (total: 3,701 chromosomes). Considering the most frequent haplotype in each population discloses a clearly discontinuous pattern, the Euro-Asian groups presenting higher than 50 percent of their specific (Arab-Asian) haplotype, Africans three distinct categories (respectively higher prevalences of the Bantu, Benin and Senegal haplotypes), and the Americas showing higher frequencies of Benin in the North and Caribbean area, and Bantu in Mexico and Brazil. A dendrogram confirms these results, with the American populations being placed in an intermediary position. Genetic diversity analysis did not clearly separate the African clusters. Total diversity was similar in Africa and the Americas (0.689 and 0.622, respectively), with a higher interpopulation diversity in the former (62 percent versus 12 percent). Total genetic diversity considering Brazil only, as opposed to all America, yielded equivalent results (0.435, 0.622) but the interpopulation variability within Brazil is lower (6 percent versus 12 percent). Generally, the results showed a remarkable similarity with what would be expected taking into consideration the historical sources concerning African migrations.

Beta-globin gene cluster haplotypes in the Mapuche Indians of Argentina

Haplótipos derivados de cinco sítios de restriçäo polimórficos presentes no agrupamento da globina beta foram investigados em 86 cromossomos da populaçäo Mapuche da Argentina. Esses resultados foram analisados em conjunto com os previamente obtidos para dez tribos indígenas brasileiras. Oito haplótipos foram identificados, dos quais os mais freqüêntes foram o 2 (57 por cento) e o 6 (27 por cento). A presença do haplótipo 3 em 2 por cento dos cromossomos dos Mapuches é uma evidência de mistura com indivíduos de ancestralidade africana. Devido ao alto número de haplótipos, a heterozigosidade medida pelo índice Gini-Simpson é mais alta nos Mapuches do que nos índios brasileiros. A distribuçäo haplotípica nos Mapuches é também significativamente diferente da observada nas tribos brasileiras. Essa heterogeneidade poderia ser parcialmente explicada pela mistura com populaçöes näo-indígenas.

Monomorphic and polymorphic enzyme genetic markers of the Waiäpi Indians of Amapá and of inhabitants of Manaus, Amazonas

Um total de 119 índios Waiäpi e 348 habitantes de Manaus, Amazonas, foram testados usando nove sistemas genéticos enzimáticos na primeira populaçäo e dois na segunda. Os Waiäpi mostraram algumas diferenças marcantes quanto às médias dos indígenas sul-americanos em ACP*A (1 por cento vs. 14 ñ 9 por cento). GLO1*1 (9 por cento vs. 30 ñ 14 por cento) e ESD*1 e CA2*1 na populaçäo de Manaus mostraram-se dentro do intervalo encontrado previamente na regiäo norte do Brasil (ESD*1: 85 por cento vs. 80-94 por cento; CA2*1: 98 por cento vs. 89-99.8 por cento). As freqüências quase idênticas obtidas para esses dois marcadores nesta populaçäo, quando a amostra foi subdividida de acordo com a cor da pele, sugerem que tais classificaçöes morfológicas têm pouco valor nesta regiäo. Distâncias genéticas entre os Waiäpi e outras tribos, obtidas usando esses e outros marcadores genéticos, mostraram bom paralelismo com as distâncias geográficas que separam esses índios dos outros grupos considerados.

Genetic similarity and mate selection in Brazil

Mating patterns in humans may be affected by many variables. Previous findings, in paternity tests, of a higher average blood group genetic similarity for nonexcluded a compared to excluded or randomly paired individuals prompted the present studt, to verify if these results could be confirmed. A total of 769 couples was considered, the comparisons being made in relation to 14 loci which are expressed on blood. Excluded and nonexcluded, real couples and random pairs showed minimal differences in degree of genetic similarity. Humans choose their mates prefenrially but, as far these results indicate, independently of the genetic systems tested.