Genetic Assessment of Red Deer Population Structure using mtDNA

Aghazadeh, Leila (2017) Genetic Assessment of Red Deer Population Structure using mtDNA. Masters thesis, University of Mohaghegh Ardabili.

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Abstract

The breeds and sub-populations of each species are the result of mutation processes, genetic drift, natural selection, and the interaction between genetics and environment. It is a precious asset inherited from ancient times to the present generation, and its preservation has great value and importance. The genetic analysis Maral (Cervus elaphus) is essential for biodiversity conservation, knowledge about the survival of this species and identifying threatening or contributing factors in surviving the population. Therefore, the present study is carried out to identify the existing genetic mass, to study the relationship among populations, the formation and genetic variation of Iranian Maral using the sequence data of mitochondrial DNA (mtDNA) cytochrome b genes and mt DNA D-Loop region. To conduct the present research, Blood, hair or tissue samples of 78 heads Maral from 6 populations were analysed. The blood samples were collected from their jugular vein. The blood was poured into the EDTA vacuum blood collection tubes and then transferred to the laboratory until the test is carried out at -20 ° C. The DNA was isolated by a commercial kit for blood and a manual method for hair and tissue samples. Specific primers for cytochrome b and D-Loop genes were used to amplify the fragments by PCR. The amplified fragments were electrophoresed on 1.5% agarose gel. All PCR products obtained were sequenced. Then, the sequences were aligned using the BIOEDIT software to evaluate the nucleotide polymorphisms. Using the Mega software, a phylogenetic tree was drawn. The genetic population data analysis was performed by PopGene32 software. The analysis of polymorphisms were performed in DNA sequences using DnaSP. Finally, NETWORK software analyzes the network to identify haplotypic groups. The results of the sequence analysis of Maral revealed mutations that resulted in the creation of 5 haplotypes and 19 haplotypes for D-Loop region and cytochrome b gene, respectively. The haplotype diversity, nucleotide diversity and mean nucleotide difference for the D-Loop were 0.218, 0.0007 and 0.491, respectively, and for cytochrome b were 0.95, 0.0167 and 15.9, respectively. Tajima's D for the D-Loop and cytochrome b genes is -1.564 and -1.205, respectively, suggesting the presence of evolutionary forces such as inbreeding, or drift events. Genetic diversity indices show that six Maral populations are likely to experience the Battle Neck experience. The haplotypes analysis results revealed that the recent fluctuations in population size and interruption in the gene flow due to the transfer of the Marals from a population to other habitats in the past.

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