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Population Structure and History of the Sahel From the Point of View of Alcohol Metabolism
Jurišová, Lívia ; Černý, Viktor (advisor) ; Macholán, Miloš (referee)
The Sahel is the northernmost part of sub-Saharan Africa. The Sahel is inhabited by a complex mixture of people, who differ in their ethnic background, language affiliation and lifestyle. The most important and most studied gene of ethanol metabolism, ADH1B, has been understudied in the Sahel region, mainly due to the low frequency of the variant rs1229984-T, which accelerates the first step of alcohol metabolism. Due to its non- African origin, the variant rs1229984-T represents a suitable marker for population history study. The eastern Sahel is where immigrants from Arabia have been settling and mating with African populations since the 7th century CE. To study population structure and history from the point of view of alcohol meta- bolism, we have used already known genotype data from fourteen Sahelian populations, which inhabit mainly the eastern part of the region. Due to the absence of the critical locus rs1229984 in the genotyping array, the samples have been subjected to sequen- cing. Combined data from the microarray and the sequencing constituted 26 loci of the ADH1B gene and its close periphery, which came from 318 samples. Genotypic data needed to be converted into their haplotypic form by a phasing prog- ram. To choose the more appropriate phasing program, the data have been arranged...
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Migrations in the African Sahel through the view of the genetic diversity of control segment of mitochondrial DNA
Adámková, Kristýna ; Černý, Viktor (advisor) ; Frynta, Daniel (referee)
Sub-Saharan Africa is the region with the highest diversity of anatomically modern humans (AMH). With the use of genetic analysis of mostly uniparental loci, gradually we can uncover the migratory activity of humans long time ago. This work focuses on the African Sahel. It is a long, horizontal strip bordered by the Sahara Desert and tropical rainforests across the entire continent. Favorable environmental conditions and the absence of a geographical barrier are suitable not only for mobile herders, but also for sedentary farmers. These provisos create high migration aktivity in the area. In this work, I newly sequenced 474 mitochondrial DNA samples of 11 populations. Populations of pastoralists and farmers are spread all over Sahel/Savannah belt. Intrapopulation analysis assessed diversity within the population and generally showed low values in pastoral populations, especially Fulani pastoralists in the western Sahel. Interpopulation analysis revealed bigger differences between individual populations than between populations clustered in the subsistence group of pastoralists or farmers, within regions or within language. The work included populations with Afro-Asiatic, Niger-Congo and Nilo-Saharan language families. Thanks to the Migrate-n program, in this work I was able to confirm the...
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Determination of mtDNA sequence variation in czech population for the usage in forensic genetics.
Řadová, Marie ; Coufalová, Pavla (advisor) ; Vaněk, Daniel (referee)
In forensic research and practice is used an analysis of nuclear DNA commonly. However, in some cases we can use only mitochondrial DNA. The mtDNA is maternally inherited and it is located in the each cell approximately in 500 copies. Barring mutation in special noncoding segments, the mtDNA sequence of siblings and all maternal relatives is identical. This unique haplotyp can be helpful in forensic cases, such as analyzing the remains of a missing person, where known maternal relatives can provide reference samples for direct comparison to the questioned mtDNA type. MtDNA is also very resistant to the external influences, so in the cases where the amount of extracted DNA is very small or degraded it is more likely that a DNA typing result can be obtained by typing mtDNA than by typing polymorphic markers found in nuclear DNA. If we want to have a certain probability to exclude or confirm the match of two samples, classify suspect or missing person into a population, we need some enough wide comparison by the population databases. Then we can study the frequencies of different haplotypes in particular population. The aim of this thesis is summery of history of DNA analysis, mtDNA sequencing and comparison of data available in published databases in the world and mainly in the Czech Republic. There is also...
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The genetic links around the Red Sea as revealed by the mtDNA
Čížková, Martina ; Černý, Viktor (advisor) ; Rídl, Jakub (referee)
The Red Sea region is one of the important places that allow us to uncover traces of the evolution of anatomically modern humans. Besides the questions related to its expansion out of Africa, this region is also important in terms of the mutual influence between populations of Africa and Arabia that after a long period of isolation and genetic differentiation related to climate change in the Pleistocene and subsequent development of seaways and land routes in the Holocene began to contact with each other more frequently. Number of genetic analyzes has been done but some issues concerning on the later development still remain inadequately answered, mainly because of insufficient material. This work is focused on the analysis of 200 mtDNA sequences of four Sudanese populations - two populations of nomadic herdsmen Rashaida and Beja living in the close neighborhood around the city of Kassala and speaking different languages and two populations of the Nile Valley with settled way of life. Analysis of the intrapopulation level revealed much higher diversity of the sedentary populations (in this work the sedentary populations are represented by the Nubians and Arabs). Interpopulation variability and genetic distances within other 46 populations of the Red Sea showed that although Rashaida and Beja people...
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The genetic links around the Red Sea as revealed by the mtDNA
Čížková, Martina ; Černý, Viktor (advisor) ; Rídl, Jakub (referee)
The Red Sea region is one of the important places that allow us to uncover traces of the evolution of anatomically modern humans. Besides the questions related to its expansion out of Africa, this region is also important in terms of the mutual influence between populations of Africa and Arabia that after a long period of isolation and genetic differentiation related to climate change in the Pleistocene and subsequent development of seaways and land routes in the Holocene began to contact with each other more frequently. Number of genetic analyzes has been done but some issues concerning on the later development still remain inadequately answered, mainly because of insufficient material. This work is focused on the analysis of 200 mtDNA sequences of four Sudanese populations - two populations of nomadic herdsmen Rashaida and Beja living in the close neighborhood around the city of Kassala and speaking different languages and two populations of the Nile Valley with settled way of life. Analysis of the intrapopulation level revealed much higher diversity of the sedentary populations (in this work the sedentary populations are represented by the Nubians and Arabs). Interpopulation variability and genetic distances within other 46 populations of the Red Sea showed that although Rashaida and Beja people...
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Determination of mtDNA sequence variation in czech population for the usage in forensic genetics.
Řadová, Marie ; Coufalová, Pavla (advisor) ; Vaněk, Daniel (referee)
In forensic research and practice is used an analysis of nuclear DNA commonly. However, in some cases we can use only mitochondrial DNA. The mtDNA is maternally inherited and it is located in the each cell approximately in 500 copies. Barring mutation in special noncoding segments, the mtDNA sequence of siblings and all maternal relatives is identical. This unique haplotyp can be helpful in forensic cases, such as analyzing the remains of a missing person, where known maternal relatives can provide reference samples for direct comparison to the questioned mtDNA type. MtDNA is also very resistant to the external influences, so in the cases where the amount of extracted DNA is very small or degraded it is more likely that a DNA typing result can be obtained by typing mtDNA than by typing polymorphic markers found in nuclear DNA. If we want to have a certain probability to exclude or confirm the match of two samples, classify suspect or missing person into a population, we need some enough wide comparison by the population databases. Then we can study the frequencies of different haplotypes in particular population. The aim of this thesis is summery of history of DNA analysis, mtDNA sequencing and comparison of data available in published databases in the world and mainly in the Czech Republic. There is also...
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