The use of complete mitochondrial DNA to carry out phylogenetic and population genomics analyses on ancient species has shown to be successful. The relationship between modern elephants and mammoths has been elucidated thanks to analyses of genetic material coming from mammoth fossils. Similar to that here we used newly assembled complete mitogenomes from Alaskan mammoth populations from the Late Pleistocene, and publicly available mammoth mitogenome data, to assess their position within the three mitochondrial lineages previously described in the literature in a BEAST and RAxML phylogenetic tree. The studied bone fragments underwent drilling and DNA extractions before the construction of the libraries and sequencing was carried out. A novel DNA extraction method using a 96 sample plate was implemented alongside standard extraction methods. The mapping of raw reads was implemented using two BWA v0.7.18 algorithms, “aln” and “mem”. After the results of both mappings were compared, the analysis continued with the output generated by BWA aln, which had a better overall performance. The resulting phylogenetic trees had similar morphologies and placed our 10 newly assembled mitogenomes within Clade 1, a clade that was distributed throughout Eurasia and North America. Clade 1 was further divided into three subclades named Clade 1C1-C2 and 1DE. Clade 1C1 was made up of Columbian, Jeffersonian and woolly mammoth mitogenomes. One of our mitogenomes (called OG002) was placed outside of Clade 1C1, possibly due to its low coverage. Clade 1C2 was made out of North American woolly mammoths and unidentified mammoth specimens. Most of our mitogenomes (8 out of 10) were placed within this clade in the RAxML tree, and 7 out of 10 were placed within this clade in the BEAST tree. OG001 was placed outside Clade 1C2 in the BEAST tree, possibly due to its low coverage (0.9X). Clade 1DE was made up of Eurasian woolly mammoth specimens and unidentified mammoth specimens. OG020 was placed within this subclade in both trees. The current phylogenetic results were not sufficient to identify the species of our new mitogenomes, but further analysis in samples with high coverage may elucidate this matter.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-532994 |
| Date | January 2024 |
| Creators | Robles López, David Emiliano |
| Publisher | Uppsala universitet, Institutionen för geovetenskaper |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | Examensarbete vid Institutionen för geovetenskaper, 1650-6553 ; 633 |
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