DNA tests probe the genomic ancestry of Brazilians

We review studies from our laboratories using different molecular tools to characterize the ancestry of Brazilians in reference to their Amerindian, European and African roots. Initially we used uniparental DNA markers to investigate the contribution of distinct Y chromosome and mitochondrial DNA lineages to present-day populations. High levels of genetic admixture and strong directional mating between European males and Amerindian and African females were unraveled. We next analyzed different types of biparental autosomal polymorphisms. Especially useful was a set of 40 insertion-deletion polymorphisms (indels) that when studied worldwide proved exquisitely sensitive in discriminating between Amerindians, Europeans and Sub-Saharan Africans. When applied to the study of Brazilians these markers confirmed extensive genomic admixture, but also demonstrated a strong imprint of the massive European immigration wave in the 19th and 20th centuries. The high individual ancestral variability observed suggests that each Brazilian has a singular proportion of Amerindian, European and African ancestries in his mosaic genome. In Brazil, one cannot predict the color of persons from their genomic ancestry nor the opposite. Brazilians should be assessed on a personal basis, as 190 million human beings, and not as members of color groups.

Balanced polymorphism in bottlenecked populations: The case of the CCR5 5 ` cis-regulatory region in Amazonian Amerindians

The 5` cis-regulatory region of the CCR5 gene exhibits a strong signature of balancing selection in several human populations. Here we analyze the polymorphism of this region in Amerindians from Amazonia, who have a complex demographic history, including recent bottlenecks that are known to reduce genetic variability. Amerindians show high nucleotide diversity (pi = 0.27%) and significantly positive Tajima`s D, and carry haplotypes associated with weak and strong gene expression. To evaluate whether these signatures of balancing selection could be explained by demography, we perform neutrality tests based on empiric and simulated data. The observed Tajima`s D was higher than that of other world populations: higher than that found for 18 noncoding regions of South Amerindians, and higher than 99.6% of simulated genealogies, which assume nonequilibrium conditions. Moreover, comparing Amerindians and Asians, the Fst for CCR5 cis-regulatory region was unusually low, in relation to neutral markers. These findings indicate that, despite their complex demographic history, South Amerindians carry a detectable signature of selection on the CCR5 cis-regulatory region. (C) 2010 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Morfologia do cromossomo Y, função gonadal e extragonadal em touros de raças sintéticas com alterações na qualidade do sêmen

O motivo deste estudo foi o percentual elevado de descarte de touros por alterações reprodutivas, precisamente qualidade de sêmen, que se apresenta em determinados sistemas produtivos nos quais estão inseridas as raças sintéticas. Através de cinco experimentos foi permitido observar o comportamento da espermatogênese de touros de raças sintéticas do nível cromossômico ao funcional do epitélio seminífero. O experimento I, avaliou por seis meses as características seminais de 12 touros, seis de uma raça pura e seis de uma sintética, contendo em cada grupo touros aptos e inaptos a reprodução classificados por qualidade de sêmen. Os animais do grupo sintético não apresentaram recuperação das características seminais durante o período de avaliação, como os puros, indicando um quadro degenerativo permanente neste conjunto de indivíduos. O experimento II buscou identificar uma relação entre a morfologia do cromossomo Y e tipos de cruzamentos, com a qualidade seminal de touros de duas raças sintéticas, Braford e Brangus-Ibagé. A relação da morfologia do Y com a condição reprodutiva não foi comprovada, no entanto considerando os tipos de cruzamentos para obtenção de touros 3/8, os cruzamentos que utilizam fêmea ¼ com macho ½ sangue filho de Nelore proporcionam um maior percentual de animais considerados inaptos ao exame de sêmen. Este experimento sugere medidas práticas para evitar o cruzamento que traz maiores prejuízos econômicos. O experimento III foi proposto para a avaliar a intensidade de redução de células espermáticas anômalas ao longo do epidídimo em touros de uma raça sintética. A redução da freqüência de gota citoplasmática proximal foi distinta entre os grupos de touros classificados quanto a morfologia espermática e entre as regiões do epidídimo, sendo portanto um indicador sensível da qualidade espermática e classificação da fertilidade potencial de animais de raças híbridas. O experimento IV avaliou a freqüência dos túbulos seminíferos nos diferentes estádios do ciclo espermatogênico em touros de duas raças sintéticas. Nas fases iniciais do ciclo espermatogênico, todos os touros apresentam gametogênese semelhante. Nas fases em que ocorrem as divisões meióticas, os touros inaptos apresentaram maior freqüência e a na fase de maturação das espermátides os touros aptos apresentaram maior freqüência. Estes resultados indicam que nos touros inaptos ocorre um bloqueio na fase das meioses, diminuindo a freqüência dos estádios de maturação das espermátides. O experimento V identificou a expressão diferencial de um fator de crescimento (transforming growth factor alpha- TGFα) no epitélio seminífero de touros Braford e Brangus-Ibagé, aptos e inaptos à reprodução, e também avaliou a freqüência de células de Sertoli nestes animais, como um estudo inicial do controle parácrino da espermatogênese. A maior freqüência da expressão de TGFα foi observada nos estádios I e III, e também na raça Brangus-Ibagé. O número médio das células de Sertoli foi semelhante entre estádios e raças dos touros. Em todos experimentos em que as raças Braford e Brangus-Ibagé foram confrontadas, os resultados obtidos foram diferentes. As maiores freqüências de alterações na qualidade seminal não podem ser extrapoladas para todas as raças sintéticas, cabendo a prerrogativa para cada raça de um estudo específico e ajustado às suas condições de criação.

XX : XY sex chromosome system with X heterochromatinization: an early stage of sex chromosome differentiation in the Neotropic electric eel Eigenmannia virescens

An early stage of sex chromosome differentiation is reported to occur in the electric eel Eigenmannia virescens (Pisces, Sternopygidae) from populations of two tributaries of the Parana river system (Brazil). Cytogenetic studies carried out in the two populations showed that the Mogi-Guacu population is characterized by 2n = 38 chromosomes and undifferentiated sex chromosomes and the Tiete population presents 2n = 38 both for males and females and an XX:XY sex chromosome system. The X-chromosome is acrocentric, easily recognized by the presence of a conspicuous heterochromatin block in its distal portion; the Y-chromosome is probably one of the medium sized acrocentrics present in the male karyotype. BrdU induced R-bands of the two populations did not reveal any difference in the euchromatic regions of the chromosomes. AluI and HaeIII restriction enzyme digestion patterns and chromomycin A3 staining of the X-chromosome are presented. The possible role of heterochromatinization in the evolution of sex chromosomes in fish is discussed.

Comparative RH Maps of the River Buffalo and Bovine Y Chromosomes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genomic organization and comparative chromosome mapping of the U1 snRNA gene in cichlid fish, with an emphasis in Oreochromis niloticus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Fungal diversity associated with Brazilian energy transmission towers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

O cromossomo Y na raça Chianina no Brasil

Foram cariotipados 95 touros puros de origem, da raça Chianina, ditribuidos em 19 empresas pastoris, em 5 estados brasileiros. O objetivo foi investigar a incidência de indivíduos portadores de cromossomo Y acrocêntrico, típico das raças de Bos taurus indicus, face às especulações de que as raças indianas poderiam ter contribuido para a formação do Chianina. Todos os indivíduos avaliados mostraram o cromossomo Y de Bos taurrus taurus. O índice centromérico obtido foi de 43,91%, o que permitiu classificar o centrômero deste cromossomo como localizado na região mediana. Foram avaliados também 29 touros com o objetivo de verificar a presença do polimorfismo intraracial do cromossomo Y. O índice centromérico e o tamanho relativo do Y foi determinado. O tamanho do cromossomo X serviu como base para estimar o tamano relativo do Y. A análise de variância mostrou diferenças entre touros apenas no tamanho relativo do Y, sendo que o índice centromérico não difereiu entre os mesmos. Concluimos que este polimorfismo indica que a raça Chianina pode ter recebido contribuição de outras raças em passado remoto ou pode também indicar a possibilidade de cruzamentos mais recentes.

Evidence of an XX/XY sex chromosome system in the fish Dormitator maculatus (Teleostei, Eleotrididae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

On the Origin of Cattle: How Aurochs Became Cattle and Colonized the World

Since their domestication in the Neolithic, cattle have belonged to our cultural heritage. The reconstruction of their history is an active field of research 1 that contributes to our understanding of human history. Archeological data are now supplemented by analyses of modern and ancient samples of cattle with DNA markers of maternal, paternal, or autosomal inheritance. The most recent genetic data suggest that maternal lineages of taurine cattle originated in the Fertile Crescent with a possible contribution of South-European wild cattle populations, while zebu cattle originate from the Indus Valley. Subsequently, cattle accompanied human migrations, which led to the dispersal of domestic cattle of taurine, indicine, or mixed origin over Asia, Africa, Europe, and the New World. This has resulted in their adaptation to different environments and considerable variation in appearance and performance. More recently, rational management of breeding led to international movements of sires, which again changed the global patterns of genetic diversity.

Comparative Chromosome Mapping of U2 snRNA and 5S rRNA Genes in Gymnotus Species (Gymnotiformes, Gymnotidae): Evolutionary Dynamics and Sex Chromosome Linkage in G. pantanal

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Complex sex chromosome system in Eigenmannia sp. (Pisces, Gymnotiformes)

Chromosomes of Eigenmannia sp. (7 males and 15 females) collected from the Tietê River in Botucatu (SP, Brazil) were examined from gill, kidney and testicular cells. The diploid chromosome number in males was 2n=31 and in females, 2n=32. In both sexes the number of chromosomal arms was 40. The difference in diploid number was due to the fusion of two acrocentrics. Mitotic and meiotic studies suggested that one of the fused acrocentrics was the Y chromosome. The sex-determining mechanism in Eigenmannia sp. could therefore be XX, AA in the female and X, \-YA A in the males. One of the males presented 2n=30 chromosomes due to the occurrence of another fusion of acrocentrics. C-banding analysis of the mitotic chromosomes revealed constitutive heterochromatin in the centromeric regions of all acrocentrics. However, small metacentrics were C-band negative. The YA chromosome is C-band negative except for a small amount of heterochromatin in the centromeric region. The nucleolar organizer region as identified by Ag-staining is present in the interstitial region of chromosome pair No. 10. © 1984 Dr W. Junk Publishers.

Low frequency of Y anomaly detected in Australian Brahman cow-herds

Indicine cattle have lower reproductive performance in comparison to taurine. A chromosomal anomaly characterized by the presence Y markers in females was reported and associated with infertility in cattle. The aim of this study was to investigate the occurrence of the anomaly in Brahman cows. Brahman cows (n = 929) were genotyped for a Y chromosome specific region using real time-PCR. Only six out of 929 cows had the anomaly (0.6%). The anomaly frequency was much lower in Brahman cows than in the crossbred population, in which it was first detected. It also seems that the anomaly doesn't affect pregnancy in the population. Due to the low frequency, association analyses couldn't be executed. Further, SNP signal of the pseudoautosomal boundary region of the Y chromosome was investigated using HD SNP chip. Pooled DNA of non-pregnant and pregnant cows were compared and no difference in SNP allele frequency was observed. Results suggest that the anomaly had a very low frequency in this Australian Brahman population and had no effect on reproduction. Further studies comparing pregnant cows and cows that failed to conceive should be executed after better assembly and annotation of the Y chromosome in cattle.

Molecular genetic investigation of the Neolithic population history in the western Carpathian Basin

Der Fokus dieser Dissertation ist die populationsgenetische Analyse der neolithischen Bevölkerungswechsel in den 6.-5. Jahrtausende vor Christus, die im westlichen Karpatenbecken stattfanden. Die Zielsetzung der Studie war, mittels der Analyse von mitochondrialer und Y-chromosomaler aDNA, den Genpool der sechs neolithischen und kupferzeitlichen Populationen zu untersuchen und die daraus resultierenden Ergebnisse mit anderen prähistorischen und modernen genetischen Daten zu vergleichen.rnInsgesamt wurden 323 Individuen aus 32 ungarischen, kroatischen und slowakischen Fundplätzen beprobt und bearbeitet in den archäogenetischen Laboren der Johannes Gutenberg-Universität in Mainz. Die DNA Ergebnisse wurden mit verschiedenen populationsgenetischen Methoden ausgewertet. Vergleichsdaten von prähistorischen und modernen eurasiatischen Populationen wurden dazu gesammelt.rnDie HVS-I Region der mitochondrialen DNA konnten bei 256 Individuen reproduziert und authentifiziert werden (mit einer Erfolgsrate von 85.9%). Die Typisierung der HVS-II Region war in 80 Fällen erfolgreich. Testend alle gut erhaltene Proben, die Y-chromosomale Haplogruppe konnte in 33 männlichen Individuen typisiert werden.rnDie neolithischen, mitochondrialen Haplogruppen deuten auf eine hohe Variabilität des maternalen Genpools hin. Sowohl die mitochondrialen als auch die Y-chromosomalen Daten lassen Rückschlüsse auf eine nah-östliche bzw. südwestasiatische Herkunft der frühen Bauern zu. Die Starčevo- und linearbandkermaischen-Populationen in westlichem Karpatenbecken (letztere abgekürzt als LBKT) und die linearbandkermaischen-Population in Mitteleuropa (LBK) haben so starke genetische Ähnlichkeit, dass die Verbreitung der LBK nach Mitteleuropa mit vorangegangenen Wanderungsereignissen zu erklären ist. Die Transdanubische aDNA Daten zeigen hohe Affinität zu den publizierten prähistorischen aDNA Datensätzen von Mitteleuropa aus den 6.-4. Jahrtausende vor Chr. Die maternal-genetische Variabilität der Starčevo-Population konnte auch innerhalb der nachfolgenden Populationen Transdanubiens festgestellt werden. Nur kleinere Infiltrationen und Immigrationsereignissen konnten während der Vinča-, LBKT-, Sopot- und Balaton-Lasinja-Kultur in Transdanubien identifiziert werden. Zwischen den transdanubischen Regionen konnten mögliche genetische Unterschiede nur in der LBKT und in der Lengyel-Periode beobachtet werden, als sich die nördlichen Gruppen von den südlichen Populationen trennten. rnDie festgestellte Heterogenität der mtDNA in Zusammenhang mit der Y-chromosomalen Homogenität in den Starčevo- und LBK-Populationen, weisen auf patrilokale Residenzregeln und patrilineare Abstammungsregeln in den ersten Bauergemeinschaften hin. rnObwohl die hier präsentierten Daten einen großen Fortschritt in der Forschung von aDNA und Neolithikum des Karpatenbeckens und Mitteleuropas bedeuten, werfen sie auch mehrere Fragen auf, deren Beantwortung durch zukünftige Genomforschungen erbracht werden könnte.