BIOL 220 Lecture Notes - Lecture 14: Experimental Evolution, Pan-Genome, Ecotype
Lecture 14b
BIO 220
What is a Species
Evolution
Defining a species
oWith the advent of genome sequencing, scientists hoped that quantitative measures of
divergence could provide a consistent basis for defining microbial species
However there are many puzzling results
Indeed, some researchers argue that the species concept lacks meaning for
microbes
oAmong the debates, microbiologists generally agree on the importance of two
perspectives
Phylogeny
Based on DNA relatedness
Ecology
Based on shared traits and ecological niche
oAmid the debate, many microbiologist accept these three criteria for a working
definition of a species
SSU rRNA similarity is greater than or equal to 95%
Average nucleotide identity of orthologs greater than 95%
Shared ecotype between organisms with 95% or greater identity
oThis working definition classifies nearly all known bacteria in a way that reconciles
phylogeny with ecotype
oA pan-genome includes
A core genome
Which consists of genes possessed by all isolates of a species
Accessory genes which ar3e found in some isolates but not others
A pan-genome may be
Closed
ofinite set of available genes
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Document Summary
Evolution: with the advent of genome sequencing, scientists hoped that quantitative measures of divergence could provide a consistent basis for defining microbial species. Indeed, some researchers argue that the species concept lacks meaning for microbes: among the debates, microbiologists generally agree on the importance of two perspectives. Based on shared traits and ecological niche: amid the debate, many microbiologist accept these three criteria for a working definition of a species. Ssu rrna similarity is greater than or equal to 95% Average nucleotide identity of orthologs greater than 95% Shared ecotype between organisms with 95% or greater identity: this working definition classifies nearly all known bacteria in a way that reconciles phylogeny with ecotype, a pan-genome includes. Which consists of genes possessed by all isolates of a species. Accessory genes which ar3e found in some isolates but not others. Open pan-genomes predominate in nature: taxonomy is the description of distinct life forms and their organization into different categories with shared traits.
