Introduction to Phylogenetics:
Phylogenetics is the study ancestral history of a gene. Speciation events are documented in a model called the phylogenetic tree. Each branch represents a speciation event, with the less speciation events between two organisms representing a closer relationship [1]. Forming a phylogenetic tree involves determining running multiple 'bootstraps' of possible relationships to determine what relationship has the maximum likelihood of having occurred. This can be completed using a database, such as Mega11 [2].
Phylogenetics is the study ancestral history of a gene. Speciation events are documented in a model called the phylogenetic tree. Each branch represents a speciation event, with the less speciation events between two organisms representing a closer relationship [1]. Forming a phylogenetic tree involves determining running multiple 'bootstraps' of possible relationships to determine what relationship has the maximum likelihood of having occurred. This can be completed using a database, such as Mega11 [2].
Discussion:
After performing a maximum likelihood clustal omega using MEGA11 (pictured above), it is determined that PRF1 is most conserved between primates. Rodents are the next homologs with PRF1 conservation. Zebrafish is the next speciation event, with Xenopus laevis as the out-group. Primates or rodents would be the best modeling choice, however, given difficulty of housing for primates and expenses to keep rodents, zebrafish are still good candidates. This is discussed further on the homology page.
References:
[1] “Understanding Phylogenies.” Understanding Evolution, evolution.berkeley.edu/evolution-101/the-history-of-life-looking-at-the-patterns/understanding-phylogenies/. Accessed 10 Apr. 2024.
[2] MEGA11: Molecular Evolutionary Genetics Analysis version 11 (Tamura, Stecher, and Kumar 2021)
After performing a maximum likelihood clustal omega using MEGA11 (pictured above), it is determined that PRF1 is most conserved between primates. Rodents are the next homologs with PRF1 conservation. Zebrafish is the next speciation event, with Xenopus laevis as the out-group. Primates or rodents would be the best modeling choice, however, given difficulty of housing for primates and expenses to keep rodents, zebrafish are still good candidates. This is discussed further on the homology page.
References:
[1] “Understanding Phylogenies.” Understanding Evolution, evolution.berkeley.edu/evolution-101/the-history-of-life-looking-at-the-patterns/understanding-phylogenies/. Accessed 10 Apr. 2024.
[2] MEGA11: Molecular Evolutionary Genetics Analysis version 11 (Tamura, Stecher, and Kumar 2021)