Neanderthals are among the closest extinct relatives of humans and thus it is interesting to analyze the similarity with contemporary ethnic group of Homo sapiens. We devote our attention to the second pseudoautosomal region[1] (PAR2), a genomic region that presents marked structural differences among spe cies. The PAR2 of the human sexual chromosomes is located at the tip of the long arm of the X and Y chromosomes, whereas PAR1 at the short arms. Both PARs recombine during meiosis, allowing a proper distribution of chromosomes in the gametes. In this work we analysed genetic variability at PAR2 in 1,092 samples from fourteen human populations[2] and one female Neanderthal individual found in the Altai region, for which high-quality genome sequence information is available[3]. In principal component analysis the first component separates Africans from the other populations while the second separates Asians from Europeans, as usually observed in other regions of the genome. In this context, the Neanderthal is clearly placed among the Africans but it is not evident which population she belongs to. We thus considered a support-vector machines (SVM)[4] algorithm as a further system of automatic classification. We trained the algorithm with respect to both continents and populations, and we checked the quality using ten-fold cross validation[5]. This classification confirms higher similarity of Neanderthals to the Africans, with respect to other continental populations, and it places Neanderthal among Yorubans within Africa (see table). This work shows for the first time that the PAR2 region classifies humans as other autosomal regions, and that genetic variability within humans mostly reflect what is observed in the rest of the genome. We expected Neanderthal to be equally distant from all the continental populations, but surprisingly her genome is closer to Africans than to other populations that separated from Africans in very recent time. This might reflect high genetic drift and a founder effect in the ancestors of Asians and Europeans that migrated out of Africa around 50,000 years ago. Finally, we also demonstrated when few genetic markers are available, a more accurate classification might be obtained applying SVM algorithms.
Genetic variability at the second pseudoautosomal region in ancient and modern humans
Marcella Vacca;Maurizio D'Esposito;
2014
Abstract
Neanderthals are among the closest extinct relatives of humans and thus it is interesting to analyze the similarity with contemporary ethnic group of Homo sapiens. We devote our attention to the second pseudoautosomal region[1] (PAR2), a genomic region that presents marked structural differences among spe cies. The PAR2 of the human sexual chromosomes is located at the tip of the long arm of the X and Y chromosomes, whereas PAR1 at the short arms. Both PARs recombine during meiosis, allowing a proper distribution of chromosomes in the gametes. In this work we analysed genetic variability at PAR2 in 1,092 samples from fourteen human populations[2] and one female Neanderthal individual found in the Altai region, for which high-quality genome sequence information is available[3]. In principal component analysis the first component separates Africans from the other populations while the second separates Asians from Europeans, as usually observed in other regions of the genome. In this context, the Neanderthal is clearly placed among the Africans but it is not evident which population she belongs to. We thus considered a support-vector machines (SVM)[4] algorithm as a further system of automatic classification. We trained the algorithm with respect to both continents and populations, and we checked the quality using ten-fold cross validation[5]. This classification confirms higher similarity of Neanderthals to the Africans, with respect to other continental populations, and it places Neanderthal among Yorubans within Africa (see table). This work shows for the first time that the PAR2 region classifies humans as other autosomal regions, and that genetic variability within humans mostly reflect what is observed in the rest of the genome. We expected Neanderthal to be equally distant from all the continental populations, but surprisingly her genome is closer to Africans than to other populations that separated from Africans in very recent time. This might reflect high genetic drift and a founder effect in the ancestors of Asians and Europeans that migrated out of Africa around 50,000 years ago. Finally, we also demonstrated when few genetic markers are available, a more accurate classification might be obtained applying SVM algorithms.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
