Biology subjects

Birky, C. W.

Publications and source records attributed to Birky, C. W..

2 recordsLinked to original sources

bioRxiv2021

KoT: an automatic implementation of the K/θ method for species delimitation

AO_SCPLOWBSTRACTC_SCPLOWK/{theta} is a method to delineate species that rests on the calculation of the ratio between the average distance K separating two putative species-level clades and the genetic diversity{theta} of these clades. Although this method is explicitly rooted in population genetic theory, it was never benchmarked due to the absence of a program allowing automated analyses. For the same reason, its application by hand was limited to small datasets of a few tens of sequences. We present an automatic implementation of the K/{theta} method, dubbed KoT (short for "K over Theta"), that takes as input a FASTA file, builds a neighbour-joining tree, and returns putative species boundaries based on a user-specified K/{theta} threshold. This automatic implementation avoids errors and makes it possible to apply the method to datasets comprising many sequences, as well as to test easily the impact of choosing different K/{theta} threshold ratios. KoT is implemented in Haxe, with a javascript webserver interface freely available at https://eeg-ebe.github.io/KoT/

evolutionary biology↗

bioRxiv2020

Evolutionary Genetic Species Detected in Prokaryotes by Applying the K/θ Ratio to DNA Sequences

Previous papers in this series described the "evolutionary genetic species concept" which is based on population genetic theory and should be applicable to any organism. Also described was a species criterion, the K/{theta} ratio, that delimits independently evolving evolutionary species based on single-gene sequences, and its application to sexual and asexual eukaryotes was illustrated. Here, we show how the evolutionary genetic species concept and the K/{theta} ratio can be applied to bacteria, using the sequences from some genes of the core genome that are rarely, if ever, transferred horizontally between different species. This completes the demonstration that K/{theta} is a general method for species delimitation, applicable to all organisms. Also, it adds to the evidence that bacteria have species in the most general sense, even though they have the ability to exchange genes across species boundaries. Finally, we show that a published critique of the use of K/{theta} [≥] 4 as a criterion for independently evolving species rests on two errors in the application of population/evolutionary genetic theory.

evolutionary biology↗