| Abstract | Cijeli mitogenom goveda kroz analizu haplotipova/haplogrupa pruža uvide u evoluciju, filogeografiju i genetičku raznolikost različitih pasmina. U ovom diplomskom radu analiziran je set novodostupnih mitogenoma u GenBank repozitoriju koji se sastojao od 670 sekvenci dužine 16338 parova baza zajedno s referentnim mitogenomom V00654 i 33 referenta mitogenoma kao predstavnike T1, T2, T3, T4, T5, I ,P, R, Q haplogrupa. Set je obuhvatio 77 pasmina raspoređenih kroz 22 države od čega su najzastupljenije Indija s 343, Kina s 271 i Mongolija s 27 jedinki. Identificirano je ukupno 1433 varijabilna mjesta od čega je 788 parsim informativnih i 645 singleton mjesta te je izračunat 481 haplotip uz visoku raznolikost haplotipova od 0.9966. Analiza p-distanci otkrila je veće razlike između određenih kineskih i indijskih pasmina, kao i između indijskih i europskih pasmina. Beast filogenetska analiza klasificirala je 334 mitogenoma u haplogrupu I1, 119 u I2 i 176 mitogenoma u T3 haplogrupu kao najfrekventnije, a filogeografska distribucija navedenih haplogrupa je pokazala da u Kini 110 mitogenoma pripada haplogrupi I1, 93 haplogrupi T3 i 11 hapogrupi I2, u Indiji 219 haplogrupi I1, 105 haplogrupi I2 i 17 haplogrupi T3 te u Mongoliji 12 mitogenoma haplogrupi T3, sedam haplogrupi T2, šest haplogrupo T4 i dva haplogrupi I1. Također, analizom velikog broja mitogenoma haplogrupe I u Beast filogenetskom stablu uočena je pojava četiri subhaplogrupe koje su odvojene s posteriori vjerojatnošću 0.95 što bi moglo predstavljati osnovu za reklasifikaciju I1 i I2 u više subhaplogrupa. Ista podjela I haplogrupe na četiri subhaplogrupe potvrđena je median-joining mrežom uz jasno odvajanje od ostalih haplogrupa. Rezultati MJ mreže i filogenetskog stabla ukazali su na značajnu razliku između haplogrupa I i T3, potvrđujući da su pasmine haplogrupe I potekle od Bos indicusa, dok su pasmine haplogrupe T3 potekle od Bos taurusa. Ova studija doprinos je razumijevanju genetičke raznolikosti i evolucijske povijesti goveda, posebno u kontekstu njihove filogeografske distribucije. |
| Abstract (english) | The whole mitochondrial genome of cattle provides insights into the evolution, phylogeography and genetic diversity of different breeds. In this thesis, a newly available set of mitochondrial genomes from the GenBank repository consisting of 670 sequences with a length of 16,338 base pairs, together with the mitochondrial reference genome V00654 and 33 mitochondrial reference genomes representing the haplogroups T1, T2, T3, T4, T5, I, P, R and Q were analysed. The set comprised 77 breeds from 22 countries, with India being the most represented with 343 individuals, followed by China with 271 and Mongolia with 27 individuals. A total of 1,433 variable sites were identified, of which 788 were parsimony informative and 645 were singleton sites. A total of 481 haplotypes were calculated, with a high haplotype diversity of 0.9966. Analysis of p-distances revealed major differences between certain Chinese and Indian breeds and between Indian and European breeds. The BEAST phylogenetic analysis classified 334 mitochondrial genomes in haplogroup I1, 119 in I2 and 176 in haplogroup T3, which is the most common. The phylogeographic distribution of these haplogroups showed that in China 110 mitochondrial genomes belonged to haplogroup I1, 93 to haplogroup T3 and 11 to haplogroup I2; in India 219 to haplogroup I1, 105 to haplogroup I2 and 17 to haplogroup T3; and in Mongolia 12 mitochondrial genomes belonged to haplogroup T3, seven to haplogroup T2, six to haplogroup T4 and two to haplogroup I1. In addition, analysis of a large number of mitochondrial genomes of haplogroup I in the BEAST phylogenetic tree revealed the appearance of four subhaplogroups separated from each other with a posterior probability of 0.95, which could form the basis for the reclassification of I1 and I2 into multiple subhaplogroups. This division of haplogroup I into four subhaplogroups was also confirmed by a median-joining network, which shows a clear separation from other haplogroups. The results of the MJ network and the phylogenetic tree indicated a significant difference between haplogroups I and T3 and confirmed that the breeds of haplogroup I descended from Bos indicus, while the breeds of haplogroup T3 descended from Bos taurus. This study contributes to the understanding of the genetic diversity and evolutionary history of cattle, especially in the context of their phylogeographic distribution. |
