Phylogeny and systematics

11 important questions on Phylogeny and systematics

What is Chatton’s prokaryote – eukaryote dichotomy based on?

Negative distinction, based on the characters that eukaryotes have but prokaryotes don’t.

Why can 16S rRNA be used as a phylogenetic marker?

It is universally distributed, functionally constant, highly conserved and an adequate length for analysis.

What do rooted trees provide that an unrooted tree does not?

Directionality and history to the taxa within the tree
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What is a big limitation of phylogenetic trees?

Recurrent mutations can erase evolutionary information, causing sequence differences to underestimate true distances

How are taxonomic species defined?

Species that are genetically cohesive, have a similar phenotype, a monophyletic group and distinctive characteristics

What other genes can be used as phylogenetic markers?

Housekeeping genes and functional genes

What would be alternatives to 16S to increase the resolution?

MLST, MLSA, single nucleotide polymorphisms, whole genome phylogeny

What is multilocus sequence typing (MLST)?

A method where allelic differences of a small number of housekeeping genes (usually 7) are analysed

What is multilocus sequence analysis (MLSA)?

the phylogenetic analysis of an concatenated protein sequence dataset (protein sequences from multiple genes/proteins joined)

What is enzyme electrophoresis (MLEE)?

A method used to analyse enzymes based on their electrophoretic mobility

What is fatty acid methyl ester (FAME)?

An analysis used for identifying microbial lipids through the analysis of fatty acid methyl esters

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