Evaluating Partial COI Phylogenetic Placement of Acinonyx jubatus Within Felidae Using In Silico Analysis

Rahadian Rasyid Alyasa (Universitas Pendidikan Indonesia)
Haibah Afifah Azmi
Amelia Pardiana Putri
Jihan Bilqis
Topik Hidayat

Journal of Biology, Environment, and Edu-Tourism
Vol. 2 No. 2 (2026): August

The cheetah (Acinonyx jubatus) possesses morphological specializations that support high-speed locomotion, while its phylogenetic position within the family Felidae has been supported by molecular studies. This study aims to evaluate the ability of partial cytochrome c oxidase subunit I (COI) fragments to reconstruct the phylogenetic placement of A. jubatus using an in silico approach. The study employed a computational molecular phylogenetic design with purposive sampling from GenBank, comprising 32 COI records—29 from Felidae and three non-Felidae outgroups within Feliformia. The sequences were aligned using MUSCLE in MEGA11, then analyzed using Maximum Parsimony, 1,000 bootstrap repetitions, the Consistency Index (CI), and the Retention Index (RI). The final 275-bp alignment contained 87 conserved positions, 188 variable positions, and 173 parsimony-informative characters; A. jubatus was placed within the Felidae ingroup with a CI of 0.429 and an RI of 0.531. These results indicate that the partial COI is effective for recovering family-level phylogenetic signals, while also providing an analytical basis for the integration of multigene data in more detailed phylogenetic studies.